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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 2
F: Trypsin

PF00089 CL0124

Representatives:

e1gdnA1[A:16-242] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TRYPSIN ; ligands: GOL,SO4 ; X-RAY DIFFRACTION 0.81Å

e2h5cA1[A:15A-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ALPHA-LYTIC PROTEASE ; ligands: GOL,SO4 ; X-RAY DIFFRACTION 0.820Å

e1gvkB1[B:16-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ELASTASE 1 ; ligands: CA,SO4 ; X-RAY DIFFRACTION 0.945Å

e1hj9A1[A:16-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BETA-TRYPSIN ; ligands: ANL,CA,GOL,SO4 ; X-RAY DIFFRACTION 0.95Å

e1a7sA1[A:1-225] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HEPARIN BINDING PROTEIN ; ligands: CL,EOH,NAG ; X-RAY DIFFRACTION 1.12Å

e1arbA1[A:1-263] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

ACHROMOBACTER PROTEASE I ; X-RAY DIFFRACTION 1.2Å

e2qaaA1[A:16-242] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

STREPTOGRISIN-B ; ligands: ACY,CL,EDO,EPE,GOL,SO4,TYR ; X-RAY DIFFRACTION 1.23Å

e1eaxA1[A:16-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SUPPRESSOR OF TUMORIGENICITY 14 ; ligands: BEN,SO4 ; X-RAY DIFFRACTION 1.300Å

e1gj7.1[A:9-18,B:16-243] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

UROKINASE-TYPE PLASMINOGEN ACTIVATOR ; ligands: 132,CIT ; X-RAY DIFFRACTION 1.33Å

e3qx5.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: 02P,GOL,NA,NAG,PO4 ; X-RAY DIFFRACTION 1.35Å

e1gvzA1[A:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

KALLIKREIN-1E2 ; ligands: ACT,GOL ; X-RAY DIFFRACTION 1.42Å

e3t5f.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Thrombin Heavy Chain & Thrombin Light Chain ; ligands: GOL,M34,NA,NAG,PO4 ; X-RAY DIFFRACTION 1.45Å

e3u98.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: BJA,NA,NAG,PO4 ; X-RAY DIFFRACTION 1.45Å

e1bioA1[A:16-243] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COMPLEMENT FACTOR D ; ligands: GOL,SOA ; X-RAY DIFFRACTION 1.5Å

e1p3cA1[A:1-215] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLUTAMYL-ENDOPEPTIDASE ; X-RAY DIFFRACTION 1.5Å

e3uwj.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Thrombin Heavy Chain & Thrombin Light Chain ; ligands: NA,NAG,PO4,TIF ; X-RAY DIFFRACTION 1.50Å

e3qto.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: 10P,GOL,NA,NAG,PO4 ; X-RAY DIFFRACTION 1.52Å

e3sha.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: GOL,NA,NAG,P97,PO4 ; X-RAY DIFFRACTION 1.52Å

e3utu.1[L:2-13,H:17-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: 1TS,NA ; X-RAY DIFFRACTION 1.55Å

e1gct.1[A:1-10,B:16-146,C:151-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GAMMA-CHYMOTRYPSIN A ; ligands: SO4 ; X-RAY DIFFRACTION 1.6Å

e2bz6H1[H:16-257] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BLOOD COAGULATION FACTOR VIIA ; ligands: 346,CA,SO4 ; X-RAY DIFFRACTION 1.6Å

e2p3uB1[B:16-243] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

COAGULATION FACTOR X ; ligands: 663,CA ; X-RAY DIFFRACTION 1.62Å

e3rlw.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Thrombin Heavy Chain & Thrombin Light Chain ; ligands: GOL,NA,NAG,PO4,S28 ; X-RAY DIFFRACTION 1.69Å

e1elvA1[A:410-668] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COMPLEMENT C1S COMPONENT ; ligands: NES,SO4 ; X-RAY DIFFRACTION 1.7Å

e1eq9A1[A:16-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CHYMOTRYPSIN ; ligands: PMS ; X-RAY DIFFRACTION 1.7Å

e2hlcA1[A:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COLLAGENASE ; X-RAY DIFFRACTION 1.7Å

e3qwc.1[L:2-13,H:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: 98P,GOL,NA,NAG ; X-RAY DIFFRACTION 1.75Å

e2gct.1[A:1-10,B:16-146,C:151-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GAMMA-CHYMOTRYPSIN A ; ligands: SO4 ; X-RAY DIFFRACTION 1.8Å

e2gmt.1[A:1-10,B:16-146,C:151-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GAMMA-CHYMOTRYPSIN ; ligands: HIN ; X-RAY DIFFRACTION 1.8Å

e2xxlA2[A:97-380] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GRAM-POSITIVE SPECIFIC SERINE PROTEASE, ISOFORM B ; ligands: CA,NAG ; X-RAY DIFFRACTION 1.8Å

e4dih.1[L:2-13,H:16-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTHROMBIN ; ligands: 0G6,CL,NA,NAG,ZN ; X-RAY DIFFRACTION 1.8Å

e1t32A1[A:16-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CATHEPSIN G ; ligands: OHH,SO4 ; X-RAY DIFFRACTION 1.85Å

e3gch.1[A:1-10,B:16-146,C:151-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GAMMA-CHYMOTRYPSIN ; ligands: OAC ; X-RAY DIFFRACTION 1.9Å

e4ax9.1[L:2-13,H:16-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTHROMBIN ; ligands: N5N,NA,NAG ; X-RAY DIFFRACTION 1.91Å

e5c2zA1[A:31-278] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Exfoliative toxin D2 ; X-RAY DIFFRACTION 1.95Å

e1ghb.1[E:1-10,F:16-146,G:151-245] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

GAMMA-CHYMOTRYPSIN ; ligands: ACE,HEX,IPA ; X-RAY DIFFRACTION 2.0Å

e1op0A1[A:16-245G] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

VENOM SERINE PROTEINASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å

e1rrkA1[A:453-739] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Complement factor B ; ligands: IOD,NA ; X-RAY DIFFRACTION 2.0Å

e2b9lA2[A:129-415] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROPHENOLOXIDASE ACTIVATING FACTOR ; ligands: CA,SO4 ; X-RAY DIFFRACTION 2.0Å

e1fiw.1[L:3-16,A:16-254] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

BETA-ACROSIN HEAVY CHAIN & BETA-ACROSIN LIGHT CHAIN ; ligands: PBZ ; X-RAY DIFFRACTION 2.1Å

e1q3xA1[A:445-686] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

MANNAN-BINDING LECTIN SERINE PROTEASE 2 ; ligands: GOL,NA ; X-RAY DIFFRACTION 2.23Å

e1azzA1[A:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

COLLAGENASE ; X-RAY DIFFRACTION 2.3Å

e1m9uA1[A:16-242] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

EARTHWORM FIBRINOLYTIC ENZYME ; X-RAY DIFFRACTION 2.3Å

e1si5H1[H:495-728] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

hepatocyte growth factor ; X-RAY DIFFRACTION 2.53Å

e1autC1[C:16-244] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

ACTIVATED PROTEIN C ; ligands: 0G6 ; X-RAY DIFFRACTION 2.8Å

e4dy7.1[A:2-13,B:16-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

THROMBIN HEAVY CHAIN & THROMBIN LIGHT CHAIN ; ligands: ACT,CA,NA ; X-RAY DIFFRACTION 2.8Å

e4f4oC2[C:103-346] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Haptoglobin ; ligands: NAG ; X-RAY DIFFRACTION 2.9Å

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: 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