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X - Possible homology level

H - Homology level

T - Topology level

F - Family level

* - Provisional representative


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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

H: RIFT-related
T: acid protease

126354, 3-crossover-4

T: double psi

152436, 2-crossover-3, 5-crossover-6

T: AbrB

122'1'344'3', 2-crossover-3, 2'-crossover-3'

T: Bacterial fluorinating enzyme-C

1265437, 2-crossover-3, 6-crossover-7

T: FMN-binding split barrel

123654, 3-crossover-4

T: Surface presentation of antigens (SPOA)

123654, 3-crossover-4, swapping

T: Alanine racemase-C

125436, 2-crossover-3, 5-crossover-6

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:

e2bmwA1[A:9-141] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FERREDOXIN--NADP REDUCTASE ; ligands: FAD ; X-RAY DIFFRACTION 1.500Å

e5mznA2[A:1177-1287] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Helicase SEN1,Helicase SEN1 ; ligands: EDO,GOL,PEG ; X-RAY DIFFRACTION 1.787Å

e4l8jA3[A:25-54,A:186-272] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Putative efflux transporter ; ligands: PEG ; X-RAY DIFFRACTION 2.06Å

e4l8jA4[A:273-350] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Putative efflux transporter ; ligands: PEG ; X-RAY DIFFRACTION 2.06Å

e3n2oA1[A:10-70,A:353-366,A:465-587] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BIOSYNTHETIC ARGININE DECARBOXYLASE ; ligands: AG2,PLP ; X-RAY DIFFRACTION 2.3Å

e3cpxA2[A:70-128] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Aminopeptidase, M42 family ; X-RAY DIFFRACTION 2.39Å

e1vf7A1[A:26-38,A:170-262] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MULTIDRUG RESISTANCE PROTEIN MEXA ; X-RAY DIFFRACTION 2.4Å

e1vf7E1[E:23-38,E:170-274] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MULTIDRUG RESISTANCE PROTEIN MEXA ; X-RAY DIFFRACTION 2.4Å

e2dpyA3[A:25-99] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Flagellum-specific ATP synthase ; X-RAY DIFFRACTION 2.4Å

e2rc5A1[A:7-150] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ferredoxin-NADP reductase ; ligands: FAD ; X-RAY DIFFRACTION 2.430Å

e6jdsA3[A:74-126] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PP1b ; X-RAY DIFFRACTION 2.50Å

e4kktD1[D:44-57,D:232-317] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MEMBRANE FUSION PROTEIN ; X-RAY DIFFRACTION 2.53Å

e3lnnA1[A:10-41,A:284-350] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like) ; ligands: ZN ; X-RAY DIFFRACTION 2.796Å

e3nzpB1[B:1-51,B:330-343,B:436-554] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ARGININE DECARBOXYLASE ; ligands: PLP,SO4 ; X-RAY DIFFRACTION 3.0Å

e4ac9C4[C:388-468] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MJ0495-LIKE PROTEIN ; ligands: SO4 ; X-RAY DIFFRACTION 3.03Å

e4dk1D1[D:34-43,D:271-328] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative MacA, Multidrug resistance protein mexA ; X-RAY DIFFRACTION 3.499Å

e4dk1D2[D:44-55,D:188-270] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative MacA, Multidrug resistance protein mexA ; X-RAY DIFFRACTION 3.499Å

e2crvA1[A:1-120] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Translation initiation factor IF-2 ; SOLUTION NMR

e3jb9X4[X:464-614] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pre-mRNA-splicing factor cwf11 ; ELECTRON MICROSCOPY

e5anbK2[K:365-609] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ELONGATION FACTOR TU GTP-BINDING DOMAIN-CONTAINING PROTEIN 1 ; ELECTRON MICROSCOPY

e6njoD2[D:34-101] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Translocator EscN ; ELECTRON MICROSCOPY

T: Aminomethyltransferase beta-barrel domain

143256, 1-crossover-2, 4-crossover-5

T: PUA domain

12543, 2-crossover-3

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