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

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

H: beta-beta-alpha zinc fingers

T: beta-beta-alpha zinc fingers

F: zf-WRNIP1_ubi

F: Zap1_zf1

F: zf_C2H2_10

F: GAGA

F: zf-C2H2_5

F: zf-C2H2_7

F: zf_Hakai

F: zf_UBZ

F: zf-H2C2_5

F: zf-C2H2_4

F: Hat1_N

F: CEP104_ZnF

F: ANM3_zf-C2H2

F: zf_C2HC_14

F: ZNF512_C2H2

F: zf_C2H2_13

F: zf-C2H2,TFIIIA_zf-C2H2

F: zf-BED

F: Sgf11,Sgf11_N

F: ROS_MUCR

F: zf-C2H2

F: UBZ_FAAP20

F: TRAF6_Z2

F: zf-U1

F: Nairovirus_Gn

F: zf-C2H2_6

F: zf-C2H2_2

F: zf-C2HE

F: TRAFD1-XIAF1_ZnF

F: zf-TRAF

F: FOXP-CC

F: zf-C2H2_jaz

F: ZNF512_zf-C2H2

F: Sgf11

F: zf-C2H2_11

F: zf-DBF

F: Sgf11_N

F: MAT1

F: zf_C2H2_6

F: zf_ZIC

F: B129_C2H2-zf

F: XAF1_C

F: zf-ACC

F: TRAF2_zf

F: zf_C2H2_ZHX

F: C2CH-4th_BIRD-IDD,C2CH-3rd_BIRD-IDD

F: Zn-C2H2_12

F: Zap1_zf2

F: Sina_ZnF

F: zf-met

F: zf-U11-48K

F: zf-H2C2_2,zf-C2H2_4

PF13465 PF13894

F: zf-H2C2_2,zf-H2C2_5

F: zf-RAG1

F: C1_2

F: ARS2

F: zf-TRAF_2

F: zf-C2H2_3

F: zf-C2H2_9

F: zf-MYST

F: zf-LYAR

F: TFIIIA_zf-C2H2

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.

Representatives:

e2j7jA2[A:1-28] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TRANSCRIPTION FACTOR IIIA ; ligands: ZN ; X-RAY DIFFRACTION 1.65Å

e5lpiC3[C:807-835] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Centrosomal protein of 104 kDa ; ligands: ZN ; X-RAY DIFFRACTION 1.80Å

e3mjhB1[B:36-69] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Early endosome antigen 1 ; ligands: ZN ; X-RAY DIFFRACTION 1.95Å

e2i13B4[B:132-168] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aart ; ligands: GOL,ZN ; X-RAY DIFFRACTION 1.96Å

e3hcsA2[A:130-156] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.15Å

e3hcuA2[A:130-159] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.60Å

e3hctA2[A:130-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.06Å

e3hcuC2[C:130-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.60Å

e3hcsB2[B:130-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.15Å

e5vo0D1[D:131-157] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 3.900Å

e5vnzA1[A:131-160] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 3.410Å

e5vnzD2[D:131-163] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 3.410Å

e5vo0A2[A:131-158] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 3.900Å

e7l3lB1[B:130-158] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.8Å

e7l3lD2[D:130-158] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.8Å

e8hz2A4[A:130-156] Image Pymol Jmol Links: PDB, SCOP, CATH

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.6Å

e8hz2B1[B:130-156] Image Pymol Jmol Links: PDB, SCOP, CATH

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.6Å

e3hcsA4[A:184-210] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 2.15Å

e2gliA3[A:135-167] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

PROTEIN (FIVE-FINGER GLI) ; ligands: CO ; X-RAY DIFFRACTION 2.600Å

e2gliA4[A:198-228] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

PROTEIN (FIVE-FINGER GLI) ; ligands: CO ; X-RAY DIFFRACTION 2.600Å

e7pp2B1[B:44-70] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AVR-Pii protein ; ligands: ZN ; X-RAY DIFFRACTION 2.69Å

e2wbtA1[A:5-99] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

B-129 ; ligands: ZN ; X-RAY DIFFRACTION 2.70Å

e5vo0D2[D:185-213] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 3.900Å

e5vo0D3[D:158-184] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TNF receptor-associated factor 6 ; ligands: ZN ; X-RAY DIFFRACTION 3.900Å

e1bhiA1[A:1-38] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CRE-BP1 ; SOLUTION NMR

e1ncsA1[A:14-60] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TRANSCRIPTIONAL FACTOR SWI5 ; ligands: ZN ; SOLUTION NMR

e1srkA1[A:1-35] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Zinc finger protein ZFPM1 ; ligands: ZN ; SOLUTION NMR

e1tf3A2[A:1-40] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TRANSCRIPTION FACTOR IIIA ; ligands: ZN ; SOLUTION NMR

e1tf3A3[A:71-101] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TRANSCRIPTION FACTOR IIIA ; ligands: ZN ; SOLUTION NMR

e1ubdC3[C:295-322] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (YY1 ZINC FINGER DOMAIN) ; ligands: ZN ; X-RAY DIFFRACTION

e1wjpA1[A:1-42] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 295 ; ligands: ZN ; SOLUTION NMR

e1wjpA3[A:67-107] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 295 ; ligands: ZN ; SOLUTION NMR

e1x3cA1[A:8-68] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 292 ; ligands: ZN ; SOLUTION NMR

e1x5wA1[A:8-35] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 64, isoforms 1 ; ligands: ZN ; SOLUTION NMR

e1x6fA1[A:8-82] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 462 ; ligands: ZN ; SOLUTION NMR

e1y0jB1[B:1-36] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Zinc-finger protein ush ; ligands: ZN ; SOLUTION NMR

e2cshA2[A:61-104] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 297B ; ligands: ZN ; SOLUTION NMR

e2cshA3[A:8-35] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 297B ; ligands: ZN ; SOLUTION NMR

e2ct1A1[A:44-71] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Transcriptional repressor CTCF ; ligands: ZN ; SOLUTION NMR

e2ct1A2[A:8-43] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Transcriptional repressor CTCF ; ligands: ZN ; SOLUTION NMR

e2ctuA1[A:1-73] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 483 ; ligands: ZN ; SOLUTION NMR

e2dlkA1[A:8-37] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

novel protein ; ligands: ZN ; SOLUTION NMR

e2dlqA3[A:8-34] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

GLI-Kruppel family member HKR3 ; ligands: ZN ; SOLUTION NMR

e2drpA1[A:103-139] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (TRAMTRACK DNA-BINDING DOMAIN) ; ligands: ZN ; X-RAY DIFFRACTION

e2encA1[A:1-46] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 224 ; ligands: ZN ; SOLUTION NMR

e2eppA1[A:286-338] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

POZ-, AT hook-, and zinc finger-containing protein 1 ; ligands: ZN ; SOLUTION NMR

e2ghfA1[A:60-95] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc fingers and homeoboxes protein 1 ; ligands: ZN ; SOLUTION NMR

e2k9hA1[A:43-71] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glycoprotein ; ligands: ZN ; SOLUTION NMR

e2k9hA2[A:72-99] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glycoprotein ; ligands: ZN ; SOLUTION NMR

e2lv2A1[A:12-54] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

INSULINOMA-ASSOCIATED PROTEIN 1 ; ligands: ZN ; SOLUTION NMR

e2ma7A2[A:1-38] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

ZINC FINGER PROTEIN EOS ; SOLUTION NMR

e2nabA1[A:1-41] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Zinc finger protein 496 ; ligands: ZN ; SOLUTION NMR

e2rpcA2[A:54-88] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Zinc finger protein ZIC 3 ; ligands: ZN ; SOLUTION NMR

e2rpcA4[A:118-155] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Zinc finger protein ZIC 3 ; ligands: ZN ; SOLUTION NMR

e2yrkA1[A:8-55] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger homeobox protein 4 ; ligands: ZN ; SOLUTION NMR

e2ytmA1[A:1-46] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Zinc finger protein 28 homolog ; ligands: ZN ; SOLUTION NMR

e2yucA2[A:43-76] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

TNF receptor-associated factor 4 ; ligands: ZN ; SOLUTION NMR

H: Expressed protein At2g23090/F21P24.15

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