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

X: cradle loop barrel

Refs: Structure 14, 1489-1498; Current opinion in structural biology 18, 358-365

X: N-terminal domain of TAP-binding protein-related

X: P22 coat protein insertion domain

X: Catalytic domain of hepatitis C virus NS2-3 protease

X: N-terminal domain of minor coat protein pIII

X: uncharacterized protein RUMGNA_01417

X: Ribosomal protein L21p

X: Ribosomal protein L25-like

X: Uncharacterized protein from gene locus rrnAC0354

X: Replication foci-targeting sequence N-terminal domain

X: Protein CLP1 C-terminal domain

X: Glycoside hydrolase family 127 C-terminal domain

X: EV matrix protein

X: LigT-like

X: Urease metallochperone UreE-N

X: Target recognition domain of zoocin A

X: Polymyxin B resistance protein

X: Cuben fold of PcncAAAD

X: OB-fold

X: GroES-like

X: Uncharacterized protein Dsy0195

X: SH3

H: SH3

H: TrmB C-terminal domain-like

H: Dom34/Pelota N-terminal domain-like

H: GatD N-terminal domain-like

H: Plus3

H: SAND

H: PRC-barrel domain

H: RNase P subunit p29

H: Central WYL domain of RspWYL1

H: Chromo domain-like

T: Chromo domain-like

lacks the first strand in SH3

F: MBT

F: Chromo

F: Tudor-knot

F: 7kD_DNA_binding

F: Chromo_shadow

Representatives:

e2fmmA1[A:108-175] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e2fmmD1[D:110-175] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e1dz1A1[A:108-171] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MODIFIER 1 PROTEIN ; SOLUTION NMR

e1s4zA1[A:108-175] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; SOLUTION NMR

e2fmmB1[B:109-175] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e1s4zB1[B:108-175] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; SOLUTION NMR

e2fmmC1[C:109-175] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e1dz1B1[B:108-171] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MODIFIER 1 PROTEIN ; SOLUTION NMR

e1e0bB1[B:266-322] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SWI6 PROTEIN ; X-RAY DIFFRACTION 1.900Å

e3kupA1[A:114-172] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 3 ; ligands: UNX ; X-RAY DIFFRACTION 1.770Å

e3p7jA1[A:141-199] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Heterochromatin protein 1 ; X-RAY DIFFRACTION 2.30Å

e3i3cA1[A:13-72] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 5 ; ligands: NA ; X-RAY DIFFRACTION 2.480Å

e3q6sA1[A:109-174] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; X-RAY DIFFRACTION 1.93Å

e3kupB1[B:112-173] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 3 ; ligands: UNX ; X-RAY DIFFRACTION 1.770Å

e3kupC1[C:112-172] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 3 ; ligands: UNX ; X-RAY DIFFRACTION 1.770Å

e3kupD1[D:114-173] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 3 ; ligands: UNX ; X-RAY DIFFRACTION 1.770Å

e3i3cB1[B:14-73] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 5 ; ligands: NA ; X-RAY DIFFRACTION 2.480Å

e3i3cC1[C:14-72] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 5 ; X-RAY DIFFRACTION 2.480Å

e3i3cD1[D:14-72] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 5 ; X-RAY DIFFRACTION 2.480Å

e3q6sC1[C:110-173] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; X-RAY DIFFRACTION 1.93Å

e3q6sD1[D:110-174] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; X-RAY DIFFRACTION 1.93Å

e3q6sB1[B:109-175] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 1 ; X-RAY DIFFRACTION 1.93Å

e3p7jB1[B:141-201] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Heterochromatin protein 1 ; ligands: GOL ; X-RAY DIFFRACTION 2.30Å

e5t1gA1[A:108-168] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 1 ; ligands: UNX ; X-RAY DIFFRACTION 1.800Å

e5t1iA1[A:109-176] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 3 ; ligands: UNX ; X-RAY DIFFRACTION 1.600Å

e5t1iB1[B:109-176] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromobox protein homolog 3 ; ligands: UNX ; X-RAY DIFFRACTION 1.600Å

e5xyvB1[B:354-417] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RHINO ; X-RAY DIFFRACTION 2.1Å

e5xywA1[A:440-493] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rhino ; X-RAY DIFFRACTION 2.7Å

e5xyvA1[A:355-417] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RHINO ; X-RAY DIFFRACTION 2.1Å

e5xywB1[B:447-492] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Rhino ; X-RAY DIFFRACTION 2.7Å

e6ftoA1[A:315-380] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromo domain-containing protein 2 ; ligands: HEZ ; X-RAY DIFFRACTION 1.6Å

e6ftoB1[B:315-380] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Chromo domain-containing protein 2 ; ligands: HEZ ; X-RAY DIFFRACTION 1.6Å

e6hw2B1[B:110-178] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 3 ; ligands: BME,CA,GOL ; X-RAY DIFFRACTION 1.941Å

e6hw2C1[C:114-176] Image Pymol Jmol Links: PDB, SCOP, CATH

Chromobox protein homolog 3 ; ligands: ACT,BME,CA,GOL ; X-RAY DIFFRACTION 1.941Å

e1e0bA1[A:262-322] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SWI6 PROTEIN ; ligands: 1PG ; X-RAY DIFFRACTION 1.900Å

F: Chromo_2

F: GEN1_C

F: LytTR

F: SAWADEE

F: MSL3_chromo-like

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.

H: ImpE-like

H: PhtA domain-like

H: Fumarylacetoacetate hydrolase, FAH, N-terminal domain

H: LexA/Signal peptidase

H: Methuselah ectodomain

H: Hypothetical protein ORF131

H: PA1645

H: Tas1 immunity protein PA14_01130

H: Auxin response factor dimerization domain and ancillary domain

H: Chromatin protein Cren7

H: Mitoribosomal protein mS34

H: Hantavirus structural glycoprotein Gn ectodomain subdomain II

H: Pyrrolysyl-tRNA synthetase tRNA binding domain

H: Insertion domain of baseplate gp8

H: Replicase polyprotein 1a N-terminal beta barrel domain

H: VP5 C-terminal C1 domain

X: IL8-related

X: UL131A-like

X: UL128 C-terminal domain

X: Cell division protein ZapC N-terminal domain

X: hypothetical protein TTMA177

X: Hantavirus structural glycoprotein Gn ectodomain subdomain III

X: MutM N-terminal domain-like

X: Ribosomal protein L14-like

X: YopX, C-terminal domain-like

X: VC0467-like

X: MMP1218-like

X: MFPT repeat

X: Barrel domain in upper collar protein

X: barrel domain in putative modulator of DNA gyrase, PmbA/TldD

X: beta-barrel domain in acetyl-CoA synthetase-like proteins

X: FimD N-terminal domain-like

X: Micronemal adhesive repeat

X: Coronavirus NSP8-like

X: PDZ domain

X: all-beta domain in DNA topoisomerase IV alpha subunit

X: hypothetical protein PA3229

X: beta-clip

X: Cyclophilin-like

X: SPOC domain-like

X: Herpes virus serine proteinase, assemblin

X: Oncogene product-like

X: Mannose 6-phosphate receptor domain

X: FMT C-terminal domain-like

X: Sortase

X: XRCC4, N-terminal domain-like

X: Virulence associated protein B (Vapb)

X: BH3618-like

X: GspC HR domain/PilP-like

X: CRISPR-Cas effector Cas13d N-terminal domain

X: Lipocalins/Streptavidin

X: YmcC-like

X: Lysosome membrane protein 2 lumenal domain

X: Handle domain in transferrin-binding protein B

X: Rubella virus capsid protein C-terminal domain

X: Single-stranded DNA-binding protein DdrB

X: Allergen Alt a 1

X: FomD-like

X: Outer membrane meander beta-barrels

X: secretin domain

X: Factor H-binding protein (fHbp) N-terminal beta-barrel domain

X: STT3/PglB/AglB beta-barrel domain

X: Acetoacetate decarboxylase-like

X: AttH-like

X: Barrel domain in heme-dependent catalases

X: WWE domain

X: GFP-like

X: Transcriptional factor tubby, C-terminal domain

X: Oxysterol-binding protein

X: CBF-like

X: NifT/FixU

X: barrel domain in CV3147-like proteins

X: Pfam PF06938 (DUF1285)

X: PH domain-like

X: Internal protein I

X: LARA domain

X: Restriction endonuclease PabI

X: N-terminal domain in DUF2118 family

X: Pestivirus Npro endopeptidase C53

X: Repulsive guidance molecule (RGM) family

X: V1/V2 domain in HIV gp120

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