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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

F: Putative_PNPOx

PF01243 CL0336

Representatives:

e1flmA1[A:1-122] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (FMN-BINDING PROTEIN) ; ligands: FMN ; X-RAY DIFFRACTION 1.20Å

e1vl7A1[A:11-145] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

hypothetical protein alr5027 ; ligands: EDO ; X-RAY DIFFRACTION 1.50Å

e2asfA1[A:11-135] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

HYPOTHETICAL PROTEIN RV2074 ; ligands: CIT ; X-RAY DIFFRACTION 1.6Å

e1w9aA1[A:6-147] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PUTATIVE PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE ; X-RAY DIFFRACTION 1.8Å

e3gasA2[A:83-249] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

HEME OXYGENASE ; ligands: AZI,EDO,HEM ; X-RAY DIFFRACTION 1.8Å

e3gasC1[C:83-249] Image Pymol Jmol Links: PDB, SCOP, CATH

HEME OXYGENASE ; ligands: AZI,EDO,HEM ; X-RAY DIFFRACTION 1.8Å

e5yjlD2[D:54-196] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamyl-tRNA reductase-binding protein ; X-RAY DIFFRACTION 2.70Å

e3gasD1[D:83-249] Image Pymol Jmol Links: PDB, SCOP, CATH

HEME OXYGENASE ; ligands: AZI,EDO,HEM ; X-RAY DIFFRACTION 1.8Å

e5yjlC2[C:56-196] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Glutamyl-tRNA reductase-binding protein ; X-RAY DIFFRACTION 2.70Å

e3gasF1[F:83-249] Image Pymol Jmol Links: PDB, SCOP, CATH

HEME OXYGENASE ; ligands: AZI,EDO,HEM ; X-RAY DIFFRACTION 1.8Å

e3gasB1[B:83-248] Image Pymol Jmol Links: PDB, SCOP, CATH

HEME OXYGENASE ; ligands: AZI,EDO,HEM ; X-RAY DIFFRACTION 1.8Å

e3gasE1[E:83-248] Image Pymol Jmol Links: PDB, SCOP, CATH

HEME OXYGENASE ; ligands: AZI,EDO,HEM ; X-RAY DIFFRACTION 1.8Å

e6vnaC1[C:9-102,C:123-156] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein ; X-RAY DIFFRACTION 2.20Å

e1rfeA1[A:3-162] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

hypothetical protein Rv2991 ; X-RAY DIFFRACTION 2.0Å

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: 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