Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

alpha bundlesalpha-helix bundles with mainly parallel helices

X: ChaB-like

X: Pilin

X: Photosystem I reaction center subunit X, PsaK

X: Photosystem I reaction center subunit XI, PsaL

X: Cell division protein CrgA

X: A hypothetical protein from Vibrio cholerae

X: C-terminal subgroup One Signature (COS) domain

X: Hsp90 co-chaperone Cdc37 N-terminal domain

X: Tas3 N-terminal domain

X: Arginine decarboxylase C-terminal helical extension

X: MERS-CoV helicase helical bundle domain

X: Anti-repressor protein

X: BRCC36 C-terminal helical domain

X: Phage G20C small terminase C-terminal domain

X: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

X: Mechanosensitive channel protein MscS (YggB), transmembrane region

X: Synaptonemal complex central element protein SYCE3

X: Protein-export membrane protein secG

X: Mitochondrial distribution and morphology protein 35

X: cytochrome bc1 complex 11 kDa protein-like

X: THO1 C-terminal domain

X: SPX domain

X: Shroom domain 2

X: immunoglobulin/albumin-binding domain-like

X: Mto2 twin-cysteine dimerization domain

X: BTA121

X: Uncharacterized protein LPG2271

X: Atg17

X: Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase

X: LYR protein

X: Mitochondrial complex I, PDSW subunit

X: alpha-helical domain in AF1104-like proteins

X: Factor H-binding protein BbCRASP-1

X: Uncharacterized protein CV0426

X: Myosin VI lever arm

X: Hypothetical protein YfhH, N-terminal domain

X: mRNA 3'-end-processing protein Rna15p hinge domain

X: Alpha-helical subdomain in E2 regularoty transactivation domain

X: Amylase-binding protein AbpA

X: Release factor (Pfam 00472) N-terminal alpha helical domain

X: Alpha-helical domain in upper collar protein

X: Ribosomal protein L19 (L19e) C-terminal domain

X: Ribosome assembly factor Efg1-like

X: First alpha-helical domain in heme-dependent catalases

X: Second alpha-helical domain in heme-dependent catalases

X: alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz

X: YqgQ-like

X: helical domain in DNA primase DnaG catalytic core

X: TAFH domain-like

X: Peroxisomal biogenesis factor 19

X: SabA N-terminal extracellular adhesion domain

X: Connexin 26

X: CFEM domain (contains eight cysteines)

X: Bromodomain-like

X: Effector SdeA helical domain

X: N-terminal domain in glucosyltransferase (Lgt1)

X: Bacterial dynamin-like protein helical domain

X: ExoU toxin middle helical domain

X: Uncharacterized protein lpg1851

X: N-terminal domain of Hypothetical protein MPN330

X: ABA-1 repeat unit

X: Charged multivesicular body protein 3 (CHMP3)-related

X: HAD superfamily helical bundle insertion domain

X: RavZ C-terminal domain

X: DH domain-like

X: Hyaluronidase domain-like

X: Putative imidazole glycerol phosphate synthase homolog (eubrec_1070)

X: Secreted protein of unknown function DUF1311

X: Uncharacterized protein AF_0924

X: Chaperone J-domain

X: Mitochondrial translocator protein (TSPO)

X: V(D)J recombination-activating protein 1 helical bundle domain

X: Rabin8 C-terminal domain

X: Four-helical up-and-down bundle

X: Palmitoyltransferase DHHC transmembrane domain

X: Stonustoxin helical domain

X: Glycogen debranching enzyme (GDE) middle domain 2

X: MtlR-like

X: Type IX secretion system component GldM helical domain

X: CRISPR/Cas system-associated protein Csm6 6H domain

X: CRISPR-Cas system RNase C2c2 N-terminal domain

X: CRISPR-Cas system first helical domain

X: CRISPR-Cas system second helical domain

X: KSHV ORF49 protein

X: GKAP homology domain 1

X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain

X: Decorin-binding protein A

X: DUF416

X: Uncharacterized conserved protein Dip1984

X: Complement regulator-acquiring surface protein 2 (CRASP-2)

X: Helical bundle insertion in helicase domains

X: Transmembrane heme-binding four-helical bundle

X: LepB GAP domain N-terminal subdomain

X: LepB GAP domain C-terminal subdomain

X: Toxin RnlA C-terminal domain

X: Middle and GTPase effector domains in dynamin-related proteins

X: Poxvirus L1 protein

X: uncharacterized putative membrane protein yfdX

X: Ranasmurfin

X: YfmB-like

X: IpaD-like

X: Imelysin peptidase-like

X: helical bundle domain in reverse transcriptase-like polymerases

X: helical domain in YacF-like proteins

X: Helical bundle in flu nucleocapsid protein

X: Integron gene cassette protein HFX_CASS2-like

X: DisA helical linker domain

X: ERO1-like

X: STAT-like

X: LIN9-LIN52 heterodimer

X: Effector protein NleF

X: Bestrophin

X: Receptor activity-modifying protein (RAMP)

X: Protein regulator of cytokinesis 1 (PRC1) dimerization domain

X: Protein regulator of cytokinesis 1 (PRC1) rod domain

X: Yersinia protein kinase A (YpkA) Rho-GTPase binding domain

X: Indolic compounds 2,3-dioxygenase-like

X: Spectrin repeat-like

X: Rev protein

X: alpha-helical protein of unknown function (Pfam01724)

X: Polarity suppression protein

X: CNOT9 binding domain CN9BD (DUF3819)

X: Nicking enzyme middle helical domain

X: Nicking enzyme C-terminal helical domain

X: Flagellar protein fliT

X: YvfG-like

X: C-terminal helical domain in Jumonji domain-containing histone demethylases

X: Domain of poly(ADP-ribose) polymerase

X: Diol dehydratase, gamma subunit

X: Glycogen synthesis protein GlgS

X: Alpha-helical domain in adenylylcyclase toxin

X: Helical bundle domain in prismane-like proteins

X: NisB C-terminal helical domain

X: Duffy-binding-like domain, N-terminal subdomain

X: Duffy-binding-like domain, C-terminal subdomain

X: Vesicular stomatitis virus L polymerase connector domain

X: AF0941-like

X: GINS helical bundle-like

X: N-cbl like

X: Membrane-integrating protein Mistic

X: Surface antigen HP0197 N-terminal domain

X: CAG pathogenicity island protein 13

X: Inositol phosphate phosphatase sopB N-terminal domain

X: DNA terminal protein C-terminal domain

X: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain

X: PH0832-like

X: ACP-like

X: Retrovirus capsid protein

X: Minor nucleoprotein VP30 C-terminal domain

X: Acyl-CoA binding protein-like

X: PAH2 domain

X: Domain of early E2A DNA-binding protein, ADDBP

X: YutG-like

X: Arp2/3 complex 21 kDa subunit ARPC3

X: Gametocyte protein Pfg27-related

X: Lv-ranaspumin (Lv-RSN-1)

X: Myosin phosphatase inhibitor 17kDa protein, CPI-17

X: ATPD N-terminal domain-like

X: CRISPR RNA silencing complex Cmr2 subunit second helical domain

X: CRISPR RNA silencing complex Cmr2 subunit first helical domain

X: Pre-mRNA-splicing factor PRP9

X: Surp module (SWAP domain)

X: C-terminal helical domain of alanine-tRNA ligase

X: LegK7, C-terminal domain

X: A DNA-binding domain in eukaryotic transcription factors

X: Hemocyanin-N

X: PTS-regulatory domain, PRD

X: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

X: Ferritin/Heme oxygenase/4-helical cytokines

X: Microtubule-Binding Domain of Flagellar Dynein

X: protein of unknown function NP_951600.1 helical domain

X: Bc28.1

X: Helical extension domain in Regulator of G-protein signaling 9

X: YfiT-like putative metal-dependent hydrolases

X: Second helical domain of Cas13b

X: UDP-galactofuranosyl transferase GlfT2 helical domain

X: Helical domain in glucansucrase GTF180

X: CH domain-like

H: Calponin-homology domain-like

H: X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain

H: Surface-layer homology (SLH) domains

T: Surface-layer homology (SLH) domains

F: SLH

PF00395

Representatives:

e3pywA1[A:3-180] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-layer protein sap ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e6bt4A1[A:38-209] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

S-layer protein sap ; ligands: KPM,SO4 ; X-RAY DIFFRACTION 2.3Å

e6cwmA1[A:28-198] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: CL ; X-RAY DIFFRACTION 1.150Å

e6cwcA1[A:28-191] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: CL,SO4 ; X-RAY DIFFRACTION 1.900Å

e6cwcB1[B:29-193] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: SO4 ; X-RAY DIFFRACTION 1.900Å

e6cwfA1[A:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 2.250Å

e6cwfB1[B:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 2.250Å

e6cwhA1[A:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 2.000Å

e6cwhB1[B:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 2.000Å

e6cwhC1[C:29-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 2.000Å

e6cwhD1[D:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 2.000Å

e6cwiA1[A:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA,SO4 ; X-RAY DIFFRACTION 2.150Å

e6cwiB1[B:29-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA,SO4 ; X-RAY DIFFRACTION 2.150Å

e6cwlA1[A:28-191] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: FHY ; X-RAY DIFFRACTION 2.150Å

e6cwlB1[B:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: FHY ; X-RAY DIFFRACTION 2.150Å

e6cwnA1[A:28-190] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA,MPD ; X-RAY DIFFRACTION 1.530Å

e6cwrA1[A:28-193] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: 6LA ; X-RAY DIFFRACTION 1.240Å

e7sv3A1[A:28-198] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: D2Y ; X-RAY DIFFRACTION 1.700Å

e7sv4A1[A:28-197] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: D4I,GOL ; X-RAY DIFFRACTION 2.060Å

e7sv5A1[A:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: D2Y,GOL ; X-RAY DIFFRACTION 1.720Å

e7sv5B1[B:28-191] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: D2Y,GOL ; X-RAY DIFFRACTION 1.720Å

e7sv6A1[A:28-192] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Surface (S-) layer glycoprotein ; ligands: D2Y ; X-RAY DIFFRACTION 1.850Å

X: Chorismate mutase II

X: uncharacterized conserved protein

X: Tetracyclin repressor-like, C-terminal domain

X: Ubiquinol-cytochrome C chaperone, C-terminal domain

X: viral membrane assembly protein A6 homolog

X: SipA N-terminal domain-like

X: Fatty acid- and retinoid-binding proteins

X: CdiI immunity protein

X: Rap2b (SMA2266)

X: Death domain-associated protein 6 histone binding domain

X: Helical domain in autophagy protein 5

X: CRISPR-associated protein Cse2

X: Regulator of G-protein signaling, RGS

X: CO dehydrogenase ISP C-domain like

X: DUF3235

X: Domain of the SRP/SRP receptor G proteins-like

X: Mechanosensory ion channel subunit mec-4 cytosolic domain

X: Drug/Metabolite transporter

X: Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain

X: Transmembrane domain of VIT1

X: Terpenoid synthases

X: Lipoprotein signal peptidase

X: Putative ECF-type Sigma Factor Negative Effector

X: Helical membrane domain in lipooligosaccharide phosphoethanolamine transferase A

X: Methyl-coenzyme M reductase alpha and beta chain-C

X: Lipoxygenase

X: all-alpha NTP pyrophosphatases

X: Phospholipase C/P1 nuclease

X: Acid phosphatase/Vanadium-dependent haloperoxidase

X: ZIP zinc transporter

X: GTPase activation domain, GAP

X: Effector protein VipE

X: PGL dimerization domain

X: PmoA

X: ADP-ribosylglycohydrolase

X: Functional domain of the splicing factor Prp18

X: Tumor necrosis factor alpha-induced protein 8-like protein 2

X: Peridinin-chlorophyll protein

X: Citrobacter dihydroxyacetone kinase extra ATP-binding domain

X: C-terminal domain of B transposition protein

X: GroEL equatorial domain-like

X: A virus capsid protein alpha-helical domain

X: Fatty acid responsive transcription factor FadR, C-terminal domain

X: C-terminal Pdr1-activating domain of J-protein Zuo1

X: Helical domain of retinal degeneration 3 protein

X: TorD-like (Pfam 06192)

X: alpha-helical domain in dehydroquinate synthase-like enzymes

X: Fic-like

X: N-terminal domain in adenosine monophosphate-protein transferase vopS

X: Topoisomerase V catalytic domain-like

X: ATP-dependent DNA ligase DNA-binding domain

X: PA2201 C-terminal domain-like

X: "fingers" domain in bacteriophage RB69-like DNA polymerase I

X: "thumb" domain in bacteriophage RB69-like DNA polymerase I

X: helical bundle domain in vacuolar ATP synthase subunit C

X: STT3/PglB/AglB transmembrane domain

X: CDP-alcohol phosphotransferase helical bundle domain

X: Na/H pumping membrane integral pyrophosphatase

X: Family A G protein-coupled receptor-like

X: Bacterial photosystem II reaction centre L and M subunits-like

X: Cytochrome c oxidase subunit III-like

X: F1F0 ATP synthase subunit A

X: Neurotransmitter-gated ion-channel transmembrane pore

X: TMEM16 lipid scramblase transmembrane domain

X: V-type ATP synthase subunit C

X: Photosystem II antenna protein-like

X: Type II ABC importer transmembrane domain fold

X: Type II ABC exporter transmembrane domain fold

X: Intramembrane protease Rce1-related

X: Multidrug efflux transporter AcrB transmembrane domain

X: Twin arginine protein translocation system component TatC

X: Integral membrane glycerol 3-phosphate acyltransferase PlsY

X: Prolipoprotein diacylglyceryl transferase

X: Membrane protein insertase YidC-related

X: Bacterial cell wall synthesis membrane enzyme MraY-related

X: GxGD membrane protease

X: N-terminal domain of Delta(14)-sterol reductase, MaSR1

X: Isoprenylcysteine carboxyl methyltransferase (ICMT)

X: Calcium release-activated calcium channel protein 1

X: Calcium ATPase transmembrane domain-related

X: Transmembrane Bax inhibitor motif (TMBIM) proteins

X: Rhomboid-like

X: Cation efflux protein transmembrane domain-like

X: Sodium/Calcium exchanger

X: Diacylglycerol kinase (DAGK)

X: Bacterial hemolysins-like

X: Putative ubiquinone biosynthesis protein

X: YP_399305.1

X: ENOD40 peptide-binding domain in sucrose synthase-1

X: N-terminal domain in fatty acid synthase subunit beta

X: Inserted helical domain in fatty acid synthase subunit beta

X: HET-S N-terminal domain

X: Peroxisomal biogenesis factor 3

X: Antitoxin VbhA

X: VP4 GT domain

X: Avirulence protein ATR13

X: Spot 14 protein

X: Integrin alpha-L cytoplasmic domain

X: Oncogenic effector CagA N-terminal domain

X: Oncogenic effector CagA domain III

X: FdhE-like

X: NADPH-cytochrome p450 reductase helical insertion domain

X: Tail specific protease helical domain

X: Primase helical domain

X: NQO2 helical bundle domain

X: Conserved type six secretion component TssL-related

X: LTXXQ motif family protein

X: Small terminase central domain

X: PH domain-containing bacterial protein oligomerization domain

X: Hypothetical protein TTHB059

X: Type III secretion protein YscE

X: Uncharacterized protein GSU0061

X: HIV Rev

X: Copper-sensitive operon repressor (CsoR)

X: Type I hyperactive antifreeze protein

X: IcmR

X: Long alpha-hairpin

X: V-type proton ATPase subunit D

X: Nucleoporin p58/p45 helical region

X: helical hairpin of HlyD-like secretion proteins

X: Kv7 proximal C-terminal Domain

X: RNA polymerase II elongation factor ELL2 C-terminal domain

X: YscO-like

X: Bacteriocin pyocin-S2 N-terminal domain

X: Prolyl 4-hydroxylase alpha subunit dimerization domain

X: TcA alpha pore-forming domain

X: Hemagglutinin HA2 chain

X: Abl interactor 2

X: Kinase suppressor of Ras 1 helical hairpin domain

X: RILP-like protein 2 N-terminal helical hairpin domain

X: Smallest capsid protein (SCP)

X: Golgi to ER traffic protein 1 cytosolic domain

X: uncharacterized protein SYNW0670

X: alpha-helical domain in type II DNA topoisomerase

X: Cyclin-dependent kinase 2-associated protein 1 C-terminal domain

X: Rad50-binding domain of Mre11

X: Nudix hydrolase N-terminal dimerization domain

X: Hypothetical protein RHA1_ro05818 N-terminal helical domain

X: Viral accessory protein x (Vpx) / viral protein r (Vpr)

X: Flagellar biosynthetic protein FliP periplasmic domain

X: Transhydrogeanse domain II

X: Helical domain in structural maintenance of chromosomes protein 3

X: Mitotic chromosome determinant-related protein N-terminal domain

X: Fluorescence recovery protein

X: Paddle domain of mitochondrial dynamin

X: Hexameric cytochrome HTHP

X: Ribosome modulation factor

X: X8 domain

X: Uncharacterized protein PP-LUZ7_gp033

X: Helical bundle domain in CusB

X: Helical domain in EHD2

X: central core domain of D-alanyl transfer protein

X: helical ridge domain of D-alanyl transfer protein

X: Helical bundle domain in S46 peptidase

X: Middle domain of hexon-associated protein (IIIa)

X: RodA transmembrane domain

X: Emopamil binding protein (EBP) transmembrane domain

X: N-terminal domain of Small RNA Degrading Nuclease (SDN)

X: Zn-binding domain in glutaminyl-tRNA synthetase

alpha superhelicesrepeating alpha-helix hairpins form a superhelix

alpha duplicates or obligate multimersalpha duplicates or monomers associate together to form a compact domain

alpha complex topologyalpha domain with complex and unique topology that cannot be described as array or bundle or superhelix

beta barrelssingle beta-sheet folded upon itself to form a barrel

beta meanderssingle beta-sheet with mainly meander topology

beta sandwichestwo beta-sheets stacked together to form a sandwich

beta duplicates or obligate multimersbeta duplicates or monomers associate together to form a compact domain

beta complex topologybeta domains with complex and unique topology that cannot be described as barrel or sandwich or meander

a+b two layersone alpha-helix layer and one beta-sheet layer

a+b three layersone mainly antiparallel beta-sheet layer sandwiched between two alpha-helix layers

a+b four layerstwo beta-sheet layers sandwiched between two alpha-helix layers

a+b complex topologyalpha and beta domain with complex and unique topology that cannot be described in layers

a+b duplicates or obligate multimersalpha and beta duplicates or monomers associated together to form a compact domain

a/b barrelsrepeating beta-alpha units form a barrel

a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers

mixed a+b and a/balpha and beta domain consists of both a+b and a/b regions

few secondary structure elementsstabilized by cofactors or disulfides

extended segmentsextended, non-globular segments, frequently bind to other proteins to form complexes

special