Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

alpha bundlesalpha-helix bundles with mainly parallel helices

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

X: C-type lectin-like

X: Noncollagenous (NC1) domain of collagen IV

X: RNase A-like

X: Procyclic specific surface antigen-2

X: Helicase Cch N-terminal domain

X: Suppressor of hydroxyurea sensitivity protein 2

X: Immune Mapped Protein 2 (IMP2)

X: USP8 interacting domain

X: PA1123-like

X: Type III R-M system modification subunit target recognition domain

X: Hemolysin II

X: Outer capsid protein VP2 body domain

X: Mitoribosomal protein mS22

X: Putative lipoprotein BA_2398

X: Head and neck region of the ectodomain of paramyxoviruses fusion glycoprotein

X: S2 subunit of coronavirus spike glycoprotein

X: nsP3 zinc-binding domain

X: Herpesvirus UL21 N-terminal domain

X: Cysteine proteinases-like

X: Late protein H7

X: Lmo1499 protein N-terminal domains

X: Lysozyme-like

X: spore cortex-lytic enzyme catalytic domain

X: Nigritoxin N-terminal domain

X: Nigritoxin C-terminal domain

X: ADP-ribosylation

X: Tic22

X: Ribosomal protein TL5/L25 C-terminal domain-like

X: Zinc finger FYVE domain-containing protein 9 C-terminal domain

X: Argininosuccinate synthetase-C

X: LCCL domain

X: Aromatic aminoacid monoxygenases, catalytic and oligomerization domains

X: Methionine synthase activation domain-like

X: Nitric oxide (NO) synthase oxygenase domain

X: Metal cation-transporting ATPase, ATP-binding domain

X: Fibrinogen C-terminal domain-like

X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

X: LDH C-terminal domain-like

X: Diaminopimelate epimerase-like

X: Anchorless fibronectin/fibrinogen binding protein C-terminal domain

X: Yos9 dimerization domain

X: Peptide deformylase

X: YrdC/RibB

X: YbaK/ProRS associated domain

X: CoA-dependent acyltransferases

X: alpha/beta-Hammerhead/Barrel-sandwich hybrid

X: DNA mimic protein DMP12-like

X: Hypothetical protein HI1480

X: RuBisCo LSMT C-terminal, substrate-binding domain

X: 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain

X: Cell cycle regulatory proteins

X: Conserved core of transcriptional regulatory protein vp16

X: Nitrile hydratase alpha chain

X: Proguanylin

X: Rotavirus NSP2 fragment, N-terminal domain

X: VSV matrix protein

X: ssRNA bacteriophage MS2 maturation protein

X: YopH tyrosine phosphatase N-terminal domain

X: Hsp33 domain

X: Outer capsid protein sigma 3-related

X: mRNA triphosphatase CET1-related

X: Phosphoinositide phosphatase SAC1 N-terminal domain

X: ParB/Sulfiredoxin

X: Aha1/BPI domain-like

X: lantibiotic self-resistance lipoprotein MlbQ

X: RGC domain

X: Transcription factor NusA, N-terminal domain

X: N-terminal subdomain in DNA replication initiator (cdc21/cdc54)

X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase

X: insertion domain in beta subunit of DNA dependent RNA-polymerase

X: barrel domain in beta subunit of DNA dependent RNA-polymerase

X: inserted a+b domain in yeast RNA polymerase beta subunit

X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase

X: N-terminal domain in RNA-polymerase beta-prime subunit

X: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit

X: first helical domain in RNA-polymerase beta-prime subunit

X: second helical domain in RNA-polymerase beta-prime subunit

X: helical domain in yeast RNA-polymerases

X: central helical domain in RNA-polymerase beta-prime subunit

X: Sandwich domain in replication terminator protein (Tus)

X: Insertion domain in replication terminator protein (Tus)

X: a+b domain in virulence-associated V antigen

X: Serpins

X: Ribonuclease P protein subunit p40

X: a+b domain in membrane penetration protein mu1

X: Inner layer core protein p3-related

X: Major inner capsid protein P1

X: L-A virus major coat protein-related

X: Major capsid protein VP5

X: MoeA domain II

X: BB1717-like

X: DNA methylase specificity domain

X: L,D-transpeptidase pre-catalytic domain-like

X: YbiA-like

X: ORC1-binding domain

X: BTG domain-like

X: DUSP, domain in ubiquitin-specific proteases

X: STIV B116-like

X: TBP-interacting protein C-terminal domain-like

X: N-terminal domain in viral ssDNA binding protein

X: first a+b domain in acetyl-CoA synthase

X: second a+b domain in acetyl-CoA synthase

X: insertion domain in bacteriophage phi29 DNA polymerase

X: linker domain in MalF N-terminal region

X: barrel domain in MalF N-terminal region

X: C-terminal a+b domain in Poly(A) polymerase catalytic subunit

X: Flu NP-like

X: Domain II in tail sheath protein Gp18

X: Flagellar protein FlgA N-terminal domain-like

X: N0 domain in phage tail proteins and secretins-like

X: C-terminal insertion domain in phage tail proteins

X: Hypothetical protein TA0956

X: Necrosis and ethylene-inducing peptide 1-like proteins

X: Envelope glycoprotein GP1

X: Arenavirus glycoprotein GP2

X: Uncharacterized protein yutD

X: Myosin VI cargo binding domain

X: MESD

X: gH main domain

X: bacteriophage phiKZ gp29PR

X: Regulatory domain of isocitrate dehydrogenase kinase/phosphatase

X: Baseplate wedge protein gp7 domain II

X: IBV Nsp2a

X: Reovirus guanylyltransferase (GTase)

X: Reovirus turret protein bridge domain

X: LidA

X: Adenine deaminase 2 C-terminal domain

X: Insertion domain in vaccinia virus scaffolding protein D13

X: Insertion domain in O-GlcNAc transferase

X: Insertion domain in Adenovirus penton base protein

X: Membrane-associated protein VP24

X: Envelope glycoprotein GP1

X: DUF2666 family proteins

X: Primosome assembly protein PriA 3' DNA-binding domain

X: P9-1

X: ArdA

X: RapA C-terminal domain

X: Polymerase acidic protein

X: Mediator of RNA polymerase II transcription submodule Med7N/31

X: Mediator co-activator domain 1 of Gal11/med15

X: Mediator of RNA polymerase II transcription subunit 11

X: Mediator of RNA polymerase II transcription subunit 22

X: Mediator of RNA polymerase II transcription subunit 8

X: Mediator of RNA polymerase II transcription subunit 17

X: Cascade subunit Csa5

X: Cas8-like

X: Scaffolding protein GPB

X: Capsid protein

X: RNAi polymerase N-terminal domain

X: Tomato mosaic virus helicase N-terminal domain

X: Oncogenic effector CagA meander beta sheet domain

X: Tetrahydrodipicolinate N-succinyletransferase N-terminal domain

X: Transcription factor tau 60 kDa subunit

X: hypothetical protein BF0379 C-terminal domain

X: SRCR-like

X: conserved hypothetical protein MTH0776

X: C-terminal domain of BipA

X: C-terminal domain of cytoplasmic dynein heavy chain

X: Protein kinase/SAICAR synthase/ATP-grasp

H: Protein kinase/SAICAR synthase/ATP-grasp

T: Protein kinase

T: SAICAR synthase

T: ATP-grasp

F: RimK

F: mRNA_cap_enzyme

F: D123

F: GSP_synth

F: Dala_Dala_lig_C

F: SPN1_m3Gcap_bd

F: RNA_lig_T4_1

F: RNA_ligase

F: TTL

F: DUF1297

F: PNKP_ligase

F: GSH_synth_ATP

F: DNA_ligase_A_M

F: GshA

F: DNA_ligase_aden

F: Lant_dehydr_N

F: DNA_ligase_aden,Nlig-Ia

PF01653 PF22745

Representatives:

e1b04B1[B:1-311] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (DNA LIGASE) ; X-RAY DIFFRACTION 2.80Å

e1v9pB3[B:2001-2317] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA LIGASE ; ligands: AMP ; X-RAY DIFFRACTION 2.9Å

e1v9pA3[A:1-317] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA LIGASE ; ligands: AMP ; X-RAY DIFFRACTION 2.9Å

e1dgsB3[B:2001-2314] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA LIGASE ; ligands: AMP ; X-RAY DIFFRACTION 2.9Å

e1b04A1[A:2-311] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (DNA LIGASE) ; X-RAY DIFFRACTION 2.80Å

e1dgsA3[A:1-314] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA LIGASE ; ligands: AMP ; X-RAY DIFFRACTION 2.9Å

e3pn1A1[A:1-318] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: IVH,IWH ; X-RAY DIFFRACTION 2.00Å

e3uq8A1[A:3-324] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: AMP,NAD ; X-RAY DIFFRACTION 1.7Å

e1zauA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: AMP ; X-RAY DIFFRACTION 3.15Å

e4glwB1[B:1-275] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: 0XT,NMN,SO4 ; X-RAY DIFFRACTION 2.000Å

e4glxA4[A:3-316] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: 0XS,SO4 ; X-RAY DIFFRACTION 1.900Å

e3sgiA3[A:8-327] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA LIGASE ; ligands: AMP ; X-RAY DIFFRACTION 3.5Å

e2owoA4[A:1-316] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: AMP,SO4 ; X-RAY DIFFRACTION 2.300Å

e4uctA1[A:1-318] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

DNA LIGASE ; ligands: 5U1,IWH ; X-RAY DIFFRACTION 2.10Å

e4ucuA1[A:1-318] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

DNA LIGASE ; ligands: 8HC,IWH ; X-RAY DIFFRACTION 2.10Å

e4ucvA1[A:1-318] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

DNA LIGASE ; ligands: I6G,IWH ; X-RAY DIFFRACTION 2.60Å

e4ucoA1[A:1-317] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

DNA LIGASE ; ligands: D41,IWH ; X-RAY DIFFRACTION 2.50Å

e4ucrA1[A:1-317] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

DNA LIGASE ; ligands: IWH,JCF ; X-RAY DIFFRACTION 2.15Å

e4ucsA1[A:1-317] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

DNA LIGASE ; ligands: 9MJ,IWH ; X-RAY DIFFRACTION 1.90Å

e4ufzA1[A:1-317] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA LIGASE ; ligands: IA7,IWH ; X-RAY DIFFRACTION 2.33Å

e5tt5A1[A:1-316] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase ; ligands: MG,NAD ; X-RAY DIFFRACTION 1.55Å

e6kduA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: AMP,NMN,SO4 ; X-RAY DIFFRACTION 2.200Å

e6kjmA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: AMP,NMN,SO4 ; X-RAY DIFFRACTION 2.200Å

e6kkvA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: DKR,SO4 ; X-RAY DIFFRACTION 2.560Å

e6krhA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: AMP,NMN,SO4 ; X-RAY DIFFRACTION 2.600Å

e6kscA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: AMP,SO4 ; X-RAY DIFFRACTION 2.400Å

e6ksdA1[A:8-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: NMN,SO4 ; X-RAY DIFFRACTION 2.500Å

e7k72A1[A:9-326] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA ligase A ; ligands: CA,MG,MPD,NAD ; X-RAY DIFFRACTION 2.050Å

e7k72B1[B:10-326] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA ligase A ; ligands: CA,MG,MPD,NAD ; X-RAY DIFFRACTION 2.050Å

e7k72C1[C:9-326] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA ligase A ; ligands: MG,MPD,NAD ; X-RAY DIFFRACTION 2.050Å

e7k72D1[D:9-326] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA ligase A ; ligands: MG,MPD,NAD ; X-RAY DIFFRACTION 2.050Å

e6lw8A1[A:9-328] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA ligase A ; ligands: EWO,GOL,SO4 ; X-RAY DIFFRACTION 2.400Å

F: ATP-grasp_4

F: ATP-grasp

F: PPDK_N

F: ATP-grasp_5

F: Ins134_P3_kin

F: GSH-S_ATP

F: GARS_A

F: MCEL_GT_NTPase

F: CP_ATPgrasp_2

F: ATP-grasp_2

F: CPSase_L_D2

F: Synapsin_C

F: ATP-grasp_3

F: Unmapped domains

Pseudo group of domains that do not map to PFam family profiles. Domains inside should not be considered as in one family.

X: 6-carboxyhexanoate-CoA ligase

X: Rifampin phosphotransferase RPH-Lm middle domain

X: TFB5-related

X: Hypothetical protein ORF126

X: FAD-binding domain-like

X: Hect, E3 ligase catalytic domain

X: E3 ubiquitin-protein ligase SopA catalytic domain

X: Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain

X: Prim-pol domain

X: Methenyltetrahydromethanopterin cyclohydrolase

X: H-NOX domain

X: pathogenicity island 3 ORF9 protein

X: VSG (variant surface glycoprotein) N-terminal domain

X: Colicin M-related

X: Polymerase cofactor VP35 C-terminal RNA binding domain

X: Phage G1 gp67

X: DNA gyrase subunit B insertion domain

X: Hypothetical protein BT3222 N-terminal domain

X: L-Lys epsilon-oxidase C-terminal domain

X: Middle domain in PB2

X: Orbivirus outer capsid protein VP5

X: Diiron beta-hydroxylase CmlA N-terminal domain

X: CRISPR-associated endonuclease Cas9 C-terminal domain

X: CRISPR-associated endonuclease Cas9 beta-hairpin domain

X: Lid domain of Cas13b

X: CRISPR-associated endonuclease Cas9 wedge domain

X: Phospholipase effector Tle1 C-terminal domain

X: Hypothetical protein lpg2422 after-hydrolase domain

X: C-terminal domain of Ebola nucleoprotein

X: Eukaryal tRNA restriction enzyme PaT

X: N-terminal domain of the pestivirus NS5B protein

X: Monotopic phosphoglycosyl transferase (PGT)-like

X: Insertion domain of minor capsid protein

X: extracellular domain of BK channel beta4 subunit

X: Helical domain of PCIF1/CAPAM

X: C-terminal domain of RNA helicase HrpB

X: RNAi suppressor protein CrPV-1A

X: head domain of ScoMcrA

X: oligomerization domain of PprA

X: SatS C-terminal domain

X: N-terminal domain of SidJ

X: Phage tail fiber assembly protein

X: C-terminal domain of DNA repair helicase RadD

X: VP5 N-terminal domain

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