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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

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

X: LuxS, MPP, ThrRS/AlaRS common domain

looks like an elaborated ferredoxin

X: ClpS-like

contains a HTH motif

X: FAD-linked reductases, C-terminal domain-like
H: FAD-linked reductases-C
T: FAD-linked reductases-C
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:

e3sm8A2[A:1213-1309] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FAD-dependent catabolic D-arginine dehydrogenase, DauA ; ligands: FNK,GOL ; X-RAY DIFFRACTION 1.07Å

e2olnA1[A:221-327] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

NIKD PROTEIN ; ligands: 6PC,FAD,NA ; X-RAY DIFFRACTION 1.15Å

e2gf3A1[A:218-321] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

MONOMERIC SARCOSINE OXIDASE ; ligands: CL,FAD,FOA,GOL ; X-RAY DIFFRACTION 1.3Å

e2f5vA1[A:355-552] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyranose 2-oxidase ; ligands: FAD,KBG ; X-RAY DIFFRACTION 1.410Å

e1kdgA1[A:513-693] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

cellobiose dehydrogenase ; ligands: 6FA,NAG ; X-RAY DIFFRACTION 1.50Å

e6cr0A2[A:279-383] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATHDOI

(S)-6-hydroxynicotine oxidase ; ligands: ACT,FAD,MPD ; X-RAY DIFFRACTION 1.548Å

e3djeA2[A:230-340] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

FRUCTOSYL AMINE: OXYGEN OXIDOREDUCTASE ; ligands: FAD,FSA ; X-RAY DIFFRACTION 1.6Å

e1pj5A3[A:220-338] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

N,N-DIMETHYLGLYCINE OXIDASE ; ligands: ACT,FAD,NA ; X-RAY DIFFRACTION 1.61Å

e3dmeA1[A:221-307] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

conserved exported protein ; ligands: FAD,TLA ; X-RAY DIFFRACTION 1.7Å

e2yr4B2[B:475-611] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pro-enzyme of L-phenylalanine oxidase ; ligands: FAD ; X-RAY DIFFRACTION 1.70Å

e2x3nA1[A:178-285] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE FAD-DEPENDENT MONOOXYGENASE ; ligands: FAD ; X-RAY DIFFRACTION 1.75Å

e5tuiB1[B:173-269] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tetracycline destructase Tet(50) ; ligands: CTC,FAD,SO4 ; X-RAY DIFFRACTION 1.75Å

e1gpeA1[A:329-524] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (GLUCOSE OXIDASE) ; ligands: FAD,NAG ; X-RAY DIFFRACTION 1.8Å

e4mifB2[B:384-556] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Pyranose 2-oxidase ; ligands: FDA ; X-RAY DIFFRACTION 1.80Å

e2dkhA2[A:223-322] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

3-hydroxybenzoate hydroxylase ; ligands: 3HB,FAD ; X-RAY DIFFRACTION 1.800Å

e5tukA1[A:175-272] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tetracycline destructase Tet(51) ; ligands: FAD,GOL ; X-RAY DIFFRACTION 1.85Å

e3c96A1[A:183-293] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Flavin-containing monooxygenase ; ligands: FAD ; X-RAY DIFFRACTION 1.9Å

e3axbA1[A:247-356] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative oxidoreductase ; ligands: EDO,FAD,PRO ; X-RAY DIFFRACTION 1.92Å

e4hb9A1[A:177-299] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Similarities with probable monooxygenase ; ligands: EDO,FAD ; X-RAY DIFFRACTION 1.93Å

e2b9wA2[A:277-373] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

putative aminooxidase ; ligands: 12P,FAD,SO4 ; X-RAY DIFFRACTION 1.95Å

e4repA2[A:302-431] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Gamma-carotene desaturase ; ligands: FAD,GOL ; X-RAY DIFFRACTION 1.970Å

e5tulA1[A:182-278] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Tetracycline destructase Tet(55) ; X-RAY DIFFRACTION 2.0Å

e5fjmA2[A:274-416] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

L-AMINO ACID DEAMINASE ; ligands: FAD ; X-RAY DIFFRACTION 2.00Å

e4u8iA1[A:291-421] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

UDP-galactopyranose mutase ; ligands: EDO,FDA,SO4 ; X-RAY DIFFRACTION 2.050Å

e3nh3X2[X:278-377] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

6-hydroxy-L-nicotine oxidase ; ligands: FAD,HNL,HNM ; X-RAY DIFFRACTION 2.10Å

e3gmbA4[A:171-274] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase ; ligands: FAD ; X-RAY DIFFRACTION 2.100Å

e3nrnA2[A:266-352] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

uncharacterized protein PF1083 ; X-RAY DIFFRACTION 2.100Å

e3i3lA2[A:181-278] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

ALKYLHALIDASE CMLS ; ligands: FAD ; X-RAY DIFFRACTION 2.2Å

e3nixB2[B:175-282] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3nixC2[C:175-284] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3nixD2[D:175-282] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3nixE2[E:175-282] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3nixF2[F:175-282] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3nixG2[G:175-282] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3nixH2[H:175-282] Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e5dbjE1[E:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase PltA ; ligands: CL,FAD ; X-RAY DIFFRACTION 2.7Å

e5dbjA2[A:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase PltA ; ligands: CL,FAD ; X-RAY DIFFRACTION 2.7Å

e5dbjB2[B:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase PltA ; ligands: CL,FAD ; X-RAY DIFFRACTION 2.7Å

e5dbjC2[C:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase PltA ; ligands: CL,FAD ; X-RAY DIFFRACTION 2.7Å

e5dbjD1[D:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase PltA ; ligands: CL,FAD ; X-RAY DIFFRACTION 2.7Å

e5bvaA2[A:172-278] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

flavin-dependent halogenase ; ligands: EDO,FAD ; X-RAY DIFFRACTION 1.87Å

e5bukA2[A:191-303] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase ; ligands: FAD ; X-RAY DIFFRACTION 1.95Å

e5bukB1[B:191-303] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FADH2-dependent halogenase ; ligands: FAD ; X-RAY DIFFRACTION 1.95Å

e5bulA2[A:172-280] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

flavin-dependent halogenase triple mutant ; ligands: FAD ; X-RAY DIFFRACTION 1.978Å

e7fcoA1[A:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH

ChlB4 ; ligands: FAD ; X-RAY DIFFRACTION 2.51Å

e7fcoB1[B:193-305] Image Pymol Jmol Links: PDB, SCOP, CATH

ChlB4 ; ligands: FAD ; X-RAY DIFFRACTION 2.51Å

e3rp6A2[A:169-272] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

FLAVOPROTEIN MONOOXYGENASE ; ligands: FAD ; X-RAY DIFFRACTION 2.2Å

e8eefA2[A:288-391] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Amine oxidase ; ligands: FAD,OTS ; X-RAY DIFFRACTION 2.21Å

e4dshA2[A:285-397] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

UDP-GALACTOPYRANOSE MUTASE ; ligands: EPE,FDA,SO4,UDP ; X-RAY DIFFRACTION 2.25Å

e3c4aA2[A:152-258] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Probable tryptophan hydroxylase vioD ; ligands: FAD ; X-RAY DIFFRACTION 2.30Å

e6iciA1[A:243-370] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

[F-actin]-monooxygenase MICAL3 ; ligands: FAD ; X-RAY DIFFRACTION 2.30Å

e4txiA1[A:238-365] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Protein-methionine sulfoxide oxidase MICAL1 ; ligands: FAD ; X-RAY DIFFRACTION 2.309Å

e5wgrA2[A:223-382] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Flavin-dependent halogenase ; ligands: CD,FAD,SO4 ; X-RAY DIFFRACTION 2.362Å

e5ez7A2[A:254-347] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

flavoenzyme PA4991 ; ligands: FAD,HG ; X-RAY DIFFRACTION 2.4Å

e6ainB1[B:185-273] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PnpA ; ligands: FAD ; X-RAY DIFFRACTION 2.48Å

e3qj4A2[A:189-294] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RENALASE ; ligands: FAD,SO4 ; X-RAY DIFFRACTION 2.5Å

e4n9xA2[A:182-282] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

PUTATIVE MONOOXYGENASE ; X-RAY DIFFRACTION 2.5Å

e1kifA1[A:195-287] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

D-AMINO ACID OXIDASE ; ligands: BEZ,FAD ; X-RAY DIFFRACTION 2.6Å

e4j2wB2[B:192-294] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Kynurenine 3-monooxygenase ; ligands: FAD ; X-RAY DIFFRACTION 2.6Å

e3nixA2[A:175-284] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Flavoprotein/dehydrogenase ; ligands: FAD ; X-RAY DIFFRACTION 2.60Å

e3ukkA2[A:291-421] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

UDP-galactopyranose mutase ; ligands: FDA,UDP ; X-RAY DIFFRACTION 2.700Å

e4eiqA3[A:185-277] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative FAD-monooxygenase ; ligands: KCT ; X-RAY DIFFRACTION 2.76Å

e2xyoA2[A:183-292] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

TETX2 ; ligands: FAD,SO4 ; X-RAY DIFFRACTION 3.00Å

e5fn0A2[A:183-298] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

KYNURENINE 3-MONOOXYGENASE ; ligands: FAD,JHY ; X-RAY DIFFRACTION 3.19Å

e5tumB2[B:171-276] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

tetracycline destructase Tet(56) ; ligands: FAD ; X-RAY DIFFRACTION 3.229Å

e3alhA1[A:192-271] * nonrep Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

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