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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

F: Asp

PF00026 CL0129

Representatives:

e1oewA2[A:1-177] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ENDOTHIAPEPSIN ; ligands: SER,SO4,THR ; X-RAY DIFFRACTION 0.91Å

e1oewA3[A:178-329] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ENDOTHIAPEPSIN ; ligands: GOL,SER,SO4,THR ; X-RAY DIFFRACTION 0.91Å

e1wkrA2[A:1-169] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYPOROPEPSIN ; ligands: SO4 ; X-RAY DIFFRACTION 1.3Å

e1wkrA3[A:170-340] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

POLYPOROPEPSIN ; ligands: SO4 ; X-RAY DIFFRACTION 1.3Å

e2qp8A2[A:245-447] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Beta-secretase 1 ; ligands: SC7 ; X-RAY DIFFRACTION 1.500Å

e2qp8A3[A:58-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Beta-secretase 1 ; ligands: SC7,TAR ; X-RAY DIFFRACTION 1.500Å

e2bjuA2[A:1-177] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PLASMEPSIN II ; ligands: IH4 ; X-RAY DIFFRACTION 1.56Å

e2bjuA3[A:178-329] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PLASMEPSIN II ; ligands: IH4 ; X-RAY DIFFRACTION 1.56Å

e1dpjA2[A:0-147] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEINASE A ; ligands: NAG ; X-RAY DIFFRACTION 1.78Å

e1dpjA3[A:148-326] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEINASE A ; ligands: NAG,SO4 ; X-RAY DIFFRACTION 1.78Å

e1j71A1[A:1-179] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aspartic proteinase ; ligands: EOH ; X-RAY DIFFRACTION 1.8Å

e1j71A2[A:180-334] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aspartic proteinase ; ligands: EOH ; X-RAY DIFFRACTION 1.8Å

e3qvcA1[A:77P-328] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HISTO-ASPARTIC PROTEASE ; ligands: EDO ; X-RAY DIFFRACTION 2.1Å

e4zl4A2[A:273-470] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Aspartic protease PM5 ; ligands: 4PK,EDO,SO4 ; X-RAY DIFFRACTION 2.37Å

e4obz.1[C:-4-98,D:106-346] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cathepsin D heavy chain & Cathepsin D light chain ; ligands: NAG ; X-RAY DIFFRACTION 2.90Å

e1mppA1[A:-1-174] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PEPSIN ; ligands: SO4 ; X-RAY DIFFRACTION

e1mppA2[A:175-332] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PEPSIN ; X-RAY DIFFRACTION

e1smrA2[A:-2-174] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RENIN ; X-RAY DIFFRACTION

e1smrA3[A:175-326] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RENIN ; X-RAY DIFFRACTION

e2aprA2[A:1-178] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RHIZOPUSPEPSIN ; ligands: CA ; X-RAY DIFFRACTION

e2aprA3[A:179-325] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RHIZOPUSPEPSIN ; ligands: CA ; X-RAY DIFFRACTION

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: 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

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