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

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

H: Lipocalins

H: Avidin/Streptavidin

H: Quinohemoprotein amine dehydrogenase A chain, domain 3-like

H: Hypothetical protein Atu4866

H: D-aminopeptidase, middle and C-terminal domains

H: Hypothetical protein TT1927B

H: YdhA-like

H: Staphostatin

H: Metalloprotease inhibitor

H: Dipeptidyl peptidase I (cathepsin C), exclusion domain

H: Hypothetical protein YwiB

H: AOC barrel-like

T: AOC barrel-like

F: Dirigent

PF03018 CL0650

Representatives:

e4revA1[A:28-184] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disease resistance response protein 206 ; ligands: GOL ; X-RAY DIFFRACTION 1.95Å

e4revB1[B:28-42,B:66-184] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Disease resistance response protein 206 ; ligands: CL,DMI,GOL ; X-RAY DIFFRACTION 1.95Å

e5lalA1[A:35-187] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein 6 ; ligands: EDO,FUC,GLY,NAG,XYP ; X-RAY DIFFRACTION 1.400Å

e5lalB1[B:33-187] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein 6 ; ligands: EDO,FUC,GLY,MAN,NAG,XYP ; X-RAY DIFFRACTION 1.400Å

e6oodA1[A:36-190] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

pterocarpan synthase dirigent protein PsPTS1 ; X-RAY DIFFRACTION 1.48Å

e6oocA1[A:23-189] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; X-RAY DIFFRACTION 2.6Å

e6oocD1[D:23-190] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; X-RAY DIFFRACTION 2.6Å

e6oocE1[E:24-191] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; X-RAY DIFFRACTION 2.6Å

e6oocC1[C:26-189] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; X-RAY DIFFRACTION 2.6Å

e6oocF1[F:24-197] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; X-RAY DIFFRACTION 2.6Å

e7r5zA1[A:14-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: CA,CL ; X-RAY DIFFRACTION 1.75Å

e7r5zC1[C:17-155] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: CA,CL ; X-RAY DIFFRACTION 1.75Å

e7yweA1[A:19-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: MPD,PO4 ; X-RAY DIFFRACTION 2.15Å

e7yweC1[C:15-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: PO4 ; X-RAY DIFFRACTION 2.15Å

e7ywfA1[A:19-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: TRS ; X-RAY DIFFRACTION 2.60Å

e7ywfC1[C:15-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: DTU ; X-RAY DIFFRACTION 2.60Å

e7r5zB1[B:6-159] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: CA,CL ; X-RAY DIFFRACTION 1.75Å

e7yweB1[B:5-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: PO4 ; X-RAY DIFFRACTION 2.15Å

e7ywfB1[B:5-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; ligands: DTU,PO4 ; X-RAY DIFFRACTION 2.60Å

e6oocB1[B:26-212] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Dirigent protein ; X-RAY DIFFRACTION 2.6Å

F: Allene_ox_cyc

F: DUF3224

F: DUF3237

F: AOC_like

H: Uncharacterized protein YLR301W

H: TLDC domain of oxidation resistance protein 2

H: Uncharacterized protein bvu_3222

H: Lipoprotein YedD

H: hypothetical protein BACEGG_01519

H: hypothetical protein SAV1798

H: Uncharacterized protein Tcur_1030

H: hypothetical protein BACUNI_03114

H: Putative lipid binding protein BT_2261

H: Hypothetical protein BT_0869

H: hypothetical protein BACOVA_00364

H: Uncharacterized protein BACOVA_03322 C-terminal domain

H: Insertion domain in tripeptidyl peptidase 2

H: LpqH

H: Barrel domain in extracellular arabinanase

H: VirK

H: PknI kinase extracellular sensor domain

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