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

H: Ferritin/Heme oxygenase

T: Ferritin

F: DUF3231

F: AOX

F: DUF2383

F: Mn_catalase

F: DUF4439

F: Ferritin

F: COQ7

F: DUF305

F: DUF5623

F: Rubrerythrin

Representatives:

e1yuzA1[A:23-166] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nigerythrin ; ligands: FE,FE2 ; X-RAY DIFFRACTION 1.4Å

e1lkoA1[A:2-147] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin all-iron(II) form ; ligands: FE2 ; X-RAY DIFFRACTION 1.63Å

e1u7mA1[A:1-53] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Four-helix bundle model ; ligands: ZN ; SOLUTION NMR

e2lfdA1[A:1-115] Image Pymol Jmol Links: PDB, SCOP, CATH

DIIRON PROTEIN ; ligands: ZN ; SOLUTION NMR

e2lffA1[A:1-115] Image Pymol Jmol Links: PDB, SCOP, CATH

DIIRON PROTEIN ; ligands: ZN ; SOLUTION NMR

e1mftA1[A:2-52] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Four-helix bundle model ; ligands: ZN ; X-RAY DIFFRACTION 2.5Å

e1mftB1[B:2-52] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Four-helix bundle model ; ligands: ZN ; X-RAY DIFFRACTION 2.5Å

e1y47A1[A:1-46] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DUEFERRI (DF2) ; ligands: CD ; X-RAY DIFFRACTION 2.7Å

e1y47B1[B:1-46] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DUEFERRI (DF2) ; ligands: CD ; X-RAY DIFFRACTION 2.7Å

e1u7mB1[B:1-53] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Four-helix bundle model ; ligands: ZN ; SOLUTION NMR

e5c39A1[A:2-52] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

P0 Manganese cluster peptide ; ligands: MN ; X-RAY DIFFRACTION 1.75Å

e5vjsA1[A:1-196] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reaction Center Maquette ; ligands: 9D7,CL,HEM,ZN ; X-RAY DIFFRACTION 2.000Å

e5vjtA1[A:1-196] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reaction Center Maquette ; ligands: CL,HEM,ZN ; X-RAY DIFFRACTION 1.450Å

e5c39B1[B:2-52] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

P0 Manganese cluster peptide ; ligands: MN ; X-RAY DIFFRACTION 1.75Å

e1rytA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RUBRERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION

e5vjuA1[A:1-196] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reaction Center Maquette Leu71His variant ; ligands: CD,HEM ; X-RAY DIFFRACTION 2.020Å

e8d9pA1[A:2-196] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reaction center maquette ; ligands: CL,HEM,MN ; X-RAY DIFFRACTION 1.90Å

e1b71A1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (RUBRERYTHRIN) ; ligands: FE,ZN ; X-RAY DIFFRACTION 1.9Å

e1qybA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RUBRERYTHRIN ; ligands: FE,SO4 ; X-RAY DIFFRACTION 1.75Å

e8d9oA1[A:1-194] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Reaction Center Maquette ; ligands: CD ; X-RAY DIFFRACTION 1.78Å

e1dvbA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RUBRERYTHRIN ; ligands: FE,ZN ; X-RAY DIFFRACTION 1.9Å

e1jybA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,ZN ; X-RAY DIFFRACTION 2.0Å

e1s30A1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RUBRERYTHRIN ; ligands: FE,ZN ; X-RAY DIFFRACTION 2.05Å

e1lkpA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: AZI,FE2 ; X-RAY DIFFRACTION 1.64Å

e1lkmA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RUBRERYTHRIN ALL-IRON(III) FORM ; ligands: FE ; X-RAY DIFFRACTION 1.69Å

e1s2zA1[A:2-147] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RUBRERYTHRIN ; ligands: FE,ZN ; X-RAY DIFFRACTION 1.75Å

e2fzfB1[B:10-167] Image Pymol Jmol Links: PDB, SCOP, CATH

hypothetical protein ; X-RAY DIFFRACTION 2.7Å

e3qhbA1[A:2-180] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYMERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION 1.2Å

e3sidA1[A:4-180] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYMERYTHRIN ; ligands: AZI,FE ; X-RAY DIFFRACTION 1.4Å

e3qhbB1[B:2-180] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYMERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION 1.2Å

e3qhcA1[A:2-180] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYMERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION 1.25Å

e3qhcB1[B:2-180] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYMERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION 1.25Å

e3sidB1[B:4-180] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SYMERYTHRIN ; ligands: AZI,FE ; X-RAY DIFFRACTION 1.4Å

e3qvdD3[D:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3pwfA3[A:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE2 ; X-RAY DIFFRACTION 1.6Å

e3pwfB3[B:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE2 ; X-RAY DIFFRACTION 1.6Å

e3pzaB3[B:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE2,PEO ; X-RAY DIFFRACTION 1.85Å

e3qvdB3[B:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3qvdH3[H:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3pzaA3[A:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE2,PEO ; X-RAY DIFFRACTION 1.85Å

e3qvdA3[A:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3qvdC3[C:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3qvdE3[E:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3qvdF3[F:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3qvdG3[G:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FE2,PEO ; X-RAY DIFFRACTION 2.0Å

e3mpsA3[A:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FEO ; X-RAY DIFFRACTION 2.0Å

e3mpsB3[B:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FEO ; X-RAY DIFFRACTION 2.0Å

e3mpsD3[D:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FEO ; X-RAY DIFFRACTION 2.0Å

e3mpsF3[F:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FEO,PEO ; X-RAY DIFFRACTION 2.0Å

e3mpsI3[I:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FEO ; X-RAY DIFFRACTION 2.0Å

e3mpsK3[K:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE,FEO,PEO ; X-RAY DIFFRACTION 2.0Å

e3mpsG3[G:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE ; X-RAY DIFFRACTION 2.0Å

e3mpsH3[H:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: FE ; X-RAY DIFFRACTION 2.0Å

e2hr5B3[B:2-134] Image Pymol Jmol Links: PDB, SCOP, CATH

RUBRERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION 2.7Å

e1nnqB3[B:2-134] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rubrerythrin ; ligands: ZN ; X-RAY DIFFRACTION 2.35Å

e2hr5A3[A:2-135] Image Pymol Jmol Links: PDB, SCOP, CATH

RUBRERYTHRIN ; ligands: FE ; X-RAY DIFFRACTION 2.7Å

e1yuxA2[A:1-163] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nigerythrin ; ligands: FE,FE2 ; X-RAY DIFFRACTION 1.6Å

e1yuxB2[B:1-163] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nigerythrin ; ligands: FE,FE2 ; X-RAY DIFFRACTION 1.6Å

e1yuzB2[B:1-163] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nigerythrin ; ligands: FE,FE2 ; X-RAY DIFFRACTION 1.4Å

e1yv1A2[A:1-163] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nigerythrin ; ligands: FE2 ; X-RAY DIFFRACTION 1.5Å

e1yv1B2[B:1-163] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Nigerythrin ; ligands: FE2 ; X-RAY DIFFRACTION 1.5Å

e2hz8A1[A:1-115] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

De novo designed diiron protein ; ligands: ZN ; SOLUTION NMR

e4di0A1[A:2-140] Image Pymol Jmol Links: PDB, SCOP, CATH

RUBRERYTHRIN ; ligands: EDO,FE ; X-RAY DIFFRACTION 1.9Å

e4di0B2[B:1-140] Image Pymol Jmol Links: PDB, SCOP, CATH

RUBRERYTHRIN ; ligands: EDO,FE,GOL ; X-RAY DIFFRACTION 1.9Å

e5n5ee1[e:2-99] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI