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

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

X: barrettide A

X: Leech antihemostatic protein

X: Plant proteinase inhibitors

X: Embryo surrounding factor (ESF) peptides

X: Type AII lantibiotic bovicin HJ50

X: PSCD domain of pleuralin-1

X: Sea anemone toxin k-like

X: Trefoil/Plexin domain-like

X: Variant surface glycoprotein MITAT 1.2, VSG 221, C-terminal domain

X: PMP inhibitors

X: Ectatomin/elicitin

X: Bowman-Birk inhibitor, BBI-like

X: DnaJ/Hsp40 cysteine-rich domain

X: P-domain of calnexin/calreticulin

X: Thyroglobulin type-1 domain

X: Shisa 3 N-terminal domain

X: TAZ domain

X: Zn-binding domain in DNA polymerase III subunits

X: N-terminal domain of helicase-loading protein DnaI

X: Tim10/DDP

X: Sec-C motif

X: Vanabin-like

X: Crambin-like

X: Blood coagulation inhibitor (disintegrin)

X: Insulin-like

X: Cellophane-induced 1 (cin1) repeats

X: Conotoxin im17a

X: Conotoxin F14

X: con-ikot-ikot toxin

X: TB module/8-cys domain

X: Phospholipase A2, PLA2

X: Zn2/Cys6 DNA-binding domain

X: HIPIP (high potential iron protein)

X: Ezh2 MCSS domain

X: C-P lyase subunit PhnJ C-terminal Zn-binding domain

X: Pre-mRNA-splicing factor BUD31

X: Protein-only RNase P Zn-binding domain

X: RelA zinc-finger domain

X: Rubredoxin-like

binds one zinc with two CxxC motifs on two beta-hairpins

X: Zinc-binding domain in Junin virus envelope glycoprotein

X: FusB family Zn-binding domain

X: Zinc finger domain in hydrogenase maturation protein HypF

X: Ribosomal protein L36

X: Btk/CHORD zinc fingers

X: CHY zinc finger

X: Trm112p-like

X: beta-barrel domain in Capz

X: Zinc hairpin stack

X: HSP33 redox switch-like

X: Coronavirus NSP10-like

X: T-antigen specific domain-like

X: Late competence protein ComFB

X: RING/U-box-like

binds two zincs. one in the same way as rubredoxin, probably related to rubredoxin. the other in a similar way as glucocorticoid receptor

H: RING/U-box-like

T: RING/U-box

T: Cysteine-rich domain

T: FYVE/PHD zinc finger

F: RING_CBP-p300

F: FYVE_2

F: zf-CW

F: ADD_ATRX

F: zf-HC5HC2H_2

F: PHD_4

F: ADD_DNMT3

Representatives:

e3a1bA1[A:472-530] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3A, Histone H3.1 ; ligands: EDO,ZN ; X-RAY DIFFRACTION 2.292Å

e8eihA2[A:414-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3B ; ligands: ZN ; ELECTRON MICROSCOPY

e8eihB2[B:414-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3B ; ligands: ZN ; ELECTRON MICROSCOPY

e8eiiA1[A:414-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eijA3[A:415-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eijB3[B:412-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eikA1[A:413-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eikB3[B:410-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eikC1[C:416-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eikE3[E:432-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e8eihC1[C:415-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3B ; ligands: ZN ; ELECTRON MICROSCOPY

e8eihD2[D:433-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3B ; ligands: ZN ; ELECTRON MICROSCOPY

e8eiiC3[C:413-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

e3a1aA2[A:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3A ; ligands: EDO,ZN ; X-RAY DIFFRACTION 2.3Å

e4u7tA3[A:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 2.90Å

e4u7tC3[C:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 2.90Å

e4u7pA3[A:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 3.820Å

e2pv0A5[A:34-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3-like ; ligands: ZN ; X-RAY DIFFRACTION 3.290Å

e2pv0C5[C:34-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3-like ; ligands: ZN ; X-RAY DIFFRACTION 3.290Å

e2pvcA5[A:34-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE ; ligands: ZN ; X-RAY DIFFRACTION 3.69Å

e2pvcB5[B:34-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE ; ligands: ZN ; X-RAY DIFFRACTION 3.69Å

e2pvcC5[C:34-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE ; ligands: ZN ; X-RAY DIFFRACTION 3.69Å

e2pv0B1[B:34-89] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3-like ; ligands: ZN ; X-RAY DIFFRACTION 3.290Å

e4qbqA1[A:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 2.4Å

e4qbqC1[C:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 2.4Å

e4qbrA2[A:475-530] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e4qbrC2[C:475-530] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 1.9Å

e4qbsA2[A:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH

DNA (cytosine-5)-methyltransferase 3A ; ligands: ZN ; X-RAY DIFFRACTION 1.8Å

e7o45A1[A:414-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Isoform 6 of DNA (cytosine-5)-methyltransferase 3B ; ligands: BR,ZN ; X-RAY DIFFRACTION 2.100Å

e7o45B2[B:414-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Isoform 6 of DNA (cytosine-5)-methyltransferase 3B ; ligands: ZN ; X-RAY DIFFRACTION 2.100Å

e7o45C1[C:414-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Isoform 6 of DNA (cytosine-5)-methyltransferase 3B ; ligands: BR,ZN ; X-RAY DIFFRACTION 2.100Å

e7o45D1[D:420-456] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Isoform 6 of DNA (cytosine-5)-methyltransferase 3B ; ligands: ZN ; X-RAY DIFFRACTION 2.100Å

e8ba5A2[A:474-530] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DNA (cytosine-5)-methyltransferase 3A ; ligands: EDO,ZN ; X-RAY DIFFRACTION 1.45Å

e8eiiB3[B:410-471] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: ZN ; ELECTRON MICROSCOPY

F: zf-CRD

PF17979 CL0361

F: RAG2_PHD

PF13341 CL0229

F: PHD_2,zf-HC5HC2H_2

F: ADDz_Dnmt3b

F: PHD_5

F: PHD

F: C5HCH

F: zf-HC5HC2H

F: zf-RING_15

F: FYVE_CARP1-2

F: PHD,zf-HC5HC2H_2

F: PHD_2

F: PHD_ash2p_like

F: PHD-1st_NSD

F: NSD_PHD

F: RIM2a_ZnF

F: STL11_N

F: FYVE

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.

T: Ariadne-1 protein homolog

only binds one zinc, structurally very different

T: AN1-like Zinc finger

T: IBR domain

H: tandem cysteine domain

X: Zinc-binding domain of DENR

X: E3 ligase HOIP C-terminal domain

X: Avirulence protein AvrP123

X: E7 C-terminal domain-like

X: C4H2C2-type zinc finger

X: Glucocorticoid receptor-like

binds zinc with one beta-hairpin and one helix, the helix binds DNA

X: CRISPR RNA silencing complex Cmr2 subunit Zn-binding domain

X: Zn3Cys9 preSET domain-related

X: Metallothionein

X: Ribosomal protein bL28-related

X: Ribosomal protein L31p

X: His-Me finger endonucleases

X: CRISPR-associated endonuclease Cpf1 nuclease domain

X: CRISPR-associated endonuclease C2c1 C-terminal domain

X: Kazal-type serine protease inhibitors-like

X: Kringle-like

X: Snake toxin-like

X: Defensin-like

X: Rattusin, a novel defensin with intermolecular disulfides

X: Epidermal patterning factor-like protein 9

X: BPTI-like

X: Cystine-knot cytokines

X: beta-beta-alpha zinc fingers

X: Inhibitor of apoptosis (IAP) repeat

X: Viral leader polypeptide zinc finger

X: Zinc finger domain in TOPLESS related protein 2 (TPR2)

X: E6 C-terminal domain-like

X: Zinc finger domain in intron-associated endonuclease 1

X: I-superfamily conotoxin r11a

X: omega toxin-like

X: Huristasin-like

X: EGF-like

X: Sortilin C-terminal domain

X: Granulin repeat

X: Conotoxin phi-MiXXVIIA

X: DPY module

X: Neurotoxin III (ATX III)

X: Hairpin loop containing domain-like

X: Fibronectin type I module-like

X: GLA-domain

X: Invertebrate chitin-binding proteins

X: Midkine-related

X: CCHC-type 1 zinc finger

X: Toxic hairpin

X: gp76 helical domain

X: lybatide 2

X: Heparin-binding domain from vascular endothelial growth factor

X: Anaphylotoxins (complement system)

X: pheromone Ep-1

X: Crustacean Hyperglycemic Hormone (CHH)-like

X: Cytochrome c oxidase subunit h

X: Frizzled cysteine-rich domain-related

X: H-NS histone-like proteins, C-terminal domain

X: p8-MTCP1-related

X: Influenza A M2 transmembrane domain

X: AapA1 toxin, transmembrane helix

X: Tetraspanin transmembrane domain

X: Tetraspanin extracellular domain

X: Ada DNA repair protein, N-terminal domain (N-Ada 10)

X: Amb V allergen

X: Apical membrane antigen 1

X: B-box zinc-binding domain-like

X: Carboxypeptidase inhibitor

X: CCCH zinc finger

X: CCHHC domain

X: Cellulose docking domain, dockering

X: Cholecystokinin A receptor, N-domain

X: Cysteine-rich DNA binding domain, (DM domain)

X: Ferredoxin thioredoxin reductase (FTR), catalytic beta chain

X: HypD Fe-S cluster binding domain

X: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit

X: HIV-1 VPU cytoplasmic domain

X: Hormone receptor domain (HRM, Pfam 02793)

X: Methylamine dehydrogenase, L chain

X: nigellin-1.1

X: Mollusk pheromone

X: Protozoan pheromone proteins

X: Necrosis inducing protein 1, NIP1

X: Lin12/Notch repeat

X: Pheromone ESP1

X: Pheromone ER-23

X: Somatomedin B domain

X: TSP type-3 repeat

X: TSP-1 type 1 repeat

X: Highly disulfide-linked beta sandwich region of p43

X: EMI domain

X: Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins

X: Type X cellulose binding domain, CBDX

X: Zinc domain conserved in yeast copper-regulated transcription factors

X: HCV NS5A domain I subdomains

X: Amino-terminal Zn-finger of Ube3a ligase (AZUL)

X: CXXC domain-like

X: PBZ domain

X: SCA7 zinc finger domain

X: Zinc binding domain of metalloprotease Spartan

X: Evasin-1

X: Elafin-like

X: Anosmin 1 N-terminal cysteine-rich domain

X: hypothetical protein NE1300

X: Bubble protein

X: Mini-collagen I, C-terminal domain

X: Fe-binding domain in prismane-like proteins

X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit

X: Fe-S cluster binding domain in some xanthine oxidase family enzymes

X: CDGSH iron-sulfur domains

X: Multiheme cytochromes

X: Dihydroorotate dehydrogenase B PyrK subunit 2Fe-2S cluster-binding domain

X: Ca-binding domain in anthrax protective antigen

X: Excalibur domain of choline binding protein L

X: Microplusin

X: CopK

X: zinc-finger domain of Nanos

X: Regulator of transcription protein Rtr1

X: Protein P16

X: Protein P30

X: PSI AB box domain

X: N-terminal A Domain of voltage-gated Ca2+ channel beta4a subunit

X: Phytotoxic protein PcF

X: Antimicrobial peptide LCI

X: 2Fe-2S binding domain in CopZ

X: Scytovirin

X: CLIP domain

X: Diapausin

X: EAGR box containing domain in MG200

X: N-terminal domain of EpCAM

X: Cys-rich region of amnionless (AMN) extracellular domain

X: Npl4 zinc binding domain

X: VWF C8-3 module

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

special