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

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

X: Rossmann-like

H: Rossmann-related

T: NAD(P)-binding Rossmann-fold domains

T: Glycosyltransferase Maf N-terminal domain

T: FAD/NAD(P)-binding domain

F: Amino_oxidase,NAD_binding_8

PF01593 PF13450

F: NAD_binding_8

PF13450 CL0063

F: OYE-like_second_a-b

F: Pyr_redox_3

F: HI0933_like

F: MCRA

F: GDI

F: FMO-like

Representatives:

e1w4xA2[A:155-389] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PHENYLACETONE MONOOXYGENASE ; ligands: FAD,SO4 ; X-RAY DIFFRACTION 1.7Å

e6hnsA1[A:170-271] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Small molecule metabolism ; ligands: NAP ; X-RAY DIFFRACTION 1.84Å

e6gqiA1[A:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: 6NA,ACT,FAD,NAP ; X-RAY DIFFRACTION 2.0Å

e6gqiB1[B:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: 6NA,FAD,NAP ; X-RAY DIFFRACTION 2.0Å

e6hnsB1[B:170-271] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Small molecule metabolism ; ligands: NAP ; X-RAY DIFFRACTION 1.84Å

e6a37A1[A:146-380] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Putative flavin-binding monooxygenase ; ligands: FAD ; X-RAY DIFFRACTION 2.20Å

e6jdkA1[A:146-383] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Baeyer-Villiger monooxygenase ; ligands: FAD ; X-RAY DIFFRACTION 2.495Å

e6jdkB2[B:146-383] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Baeyer-Villiger monooxygenase ; ligands: FAD ; X-RAY DIFFRACTION 2.495Å

e6sekA2[A:150-332] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase 5 ; ligands: EPE,FAD,GLC,LMT,NAP ; X-RAY DIFFRACTION 2.70Å

e6sekB2[B:150-332] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase 5 ; ligands: EPE,FAD,LMT,NAP ; X-RAY DIFFRACTION 2.70Å

e6semB2[B:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: FAD ; X-RAY DIFFRACTION 2.80Å

e6semA2[A:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: FAD ; X-RAY DIFFRACTION 2.80Å

e6semC2[C:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: FAD ; X-RAY DIFFRACTION 2.80Å

e6semD2[D:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: FAD ; X-RAY DIFFRACTION 2.80Å

e6sf0B2[B:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: NAP ; X-RAY DIFFRACTION 3.01Å

e6sf0A2[A:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: NAP ; X-RAY DIFFRACTION 3.01Å

e6sf0C2[C:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: NAP ; X-RAY DIFFRACTION 3.01Å

e6sf0D2[D:160-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase (FMO) 2 ; ligands: MA4,NAP ; X-RAY DIFFRACTION 3.01Å

e6wpuA1[A:187-292] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Flavin-containing monooxygenase ; ligands: SO4 ; X-RAY DIFFRACTION 2.080Å

e6kbwA2[A:171-272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Trimethylamine monooxygenase ; ligands: NAP ; X-RAY DIFFRACTION 1.6860Å

e6kbwB1[B:171-272] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Trimethylamine monooxygenase ; ligands: NAP ; X-RAY DIFFRACTION 1.6860Å

e7al4C1[C:149-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase 1 (mammalian) ; ligands: FAD,NAP ; X-RAY DIFFRACTION 3.000Å

e7al4B1[B:149-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase 1 (mammalian) ; ligands: CL,FAD,NAP ; X-RAY DIFFRACTION 3.000Å

e7al4A1[A:149-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase 1 (mammalian) ; ligands: CL,FAD,LMT,NAP ; X-RAY DIFFRACTION 3.000Å

e7al4D1[D:149-336] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Ancestral Flavin-containing monooxygenase 1 (mammalian) ; ligands: CL,FAD,GOL,LMT,NAP ; X-RAY DIFFRACTION 3.000Å

e7v8oA1[A:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: FAD,NAP ; X-RAY DIFFRACTION 2.720Å

e7v8oB1[B:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: FAD,NA,NAP,PEG ; X-RAY DIFFRACTION 2.720Å

e7v8rA2[A:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: EDO,FAD,GOL,NA,NAP ; X-RAY DIFFRACTION 1.764Å

e7v8sA1[A:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: FAD,NA,NAP ; X-RAY DIFFRACTION 2.08Å

e7v8sB2[B:148-382] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Cyclohexanone Monooxygenase from Thermocrispum municipale ; ligands: FAD,NAP ; X-RAY DIFFRACTION 2.08Å

e7v4xA1[A:146-380] Image Pymol Jmol Links: PDB, SCOP, CATH

Putative flavin-binding monooxygenase ; ligands: ATR,FAD ; X-RAY DIFFRACTION 2.33Å

e7v50A1[A:146-380] Image Pymol Jmol Links: PDB, SCOP, CATH

Putative flavin-binding monooxygenase ; ligands: FAD,NAP ; X-RAY DIFFRACTION 2.070Å

e7v51A1[A:146-380] Image Pymol Jmol Links: PDB, SCOP, CATH

Putative flavin-binding monooxygenase ; ligands: FAD ; X-RAY DIFFRACTION 2.42Å

e8b2dA1[A:170-271] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

; ligands: NAP ; X-RAY DIFFRACTION 1.62Å

F: Pyr_redox

F: SE

F: GIDA

F: Pyr_redox_2

F: Thi4

F: Trp_halogenase

F: FAD_binding_3

F: DAO

F: Pyr_redox_2,NDH2_C

PF07992 PF22366

F: Pyr_redox_2,NAD_binding_8

PF07992 PF13450

F: GMC_oxred_C

PF05199

F: GMC_oxred_N,FAD_binding_2,GMC_oxred_C

PF00732 PF00890 PF05199

F: Lys_Orn_oxgnase

F: Amino_oxidase

F: GMC_oxred_N

F: FAD_binding_2

F: FCSD_central

F: FAD_binding_3,NAD_binding_8

F: DAO,FAO_M

F: GIDA,Pyr_redox_2

F: FAD_binding_2,Pyr_redox_2

PF00890 PF07992

F: FMO-like,NAD_binding_8

PF00743 PF13450

F: GMC_oxred_N,GMC_oxred_C

PF00732 PF05199

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: Nucleotide-binding domain

T: DHS-like NAD/FAD-binding domain

T: S-adenosyl-L-methionine-dependent methyltransferases

T: Tubulin nucleotide-binding domain-like

T: NagB/RpiA/CoA transferase-like

T: MurCD/PglD N-terminal domain-like

T: Activating enzymes of the ubiquitin-like proteins

T: PreATP-grasp domain

T: Formate/glycerate dehydrogenase catalytic domain-like

T: UDPG/MGDP dehydrogenase C-terminal domain

T: Aspartate/ornithine carbamoyltransferase

H: Formate dehydrogenase/DMSO reductase, domains 2 and 3

H: Tryptophan synthase beta subunit-like PLP-dependent enzymes

H: Ribokinase-like

X: C-terminal domain in CAC2185-like proteins

X: P-loop domains-like

X: EreA/ChaN-like

X: HUP domain-like

X: HAD domain-like

X: Flavodoxin-like

X: Nucleic acid-binding domain of nonstructural protein 3

X: EDD domain

X: Phosphorylase/hydrolase-like

X: LigB-like

X: Other Rossmann-like structures with the crossover

X: N-terminal domain in NTD biosynthesis operon protein NtdA

X: Flavivirus non-structural protein 1 (NS1) a/b domain

X: STT3/PglB/AglB core domain

X: C-terminal domain in arabinosyltransferase C

X: Nqo1 FMN-binding domain-like

X: beta-carbonic anhydrase-like

X: a/b domain in QueA-like proteins (Pfam 02547)

X: a/b domain in AF0625-like proteins

X: CbiG linker domain

X: CobE/CbiG C-terminal domain-like

X: a/b domain in CV3147-like proteins

X: alpha/beta knot

X: Peptidyl-tRNA hydrolase II

X: Subtilisin-like

X: Insert domain in hypothetical protein PF0380

X: a/b domain in flagellar biosynthesis protein flhA

X: a/b domain in family 98 glycoside hydrolases

X: UPF0302 protein BA_1542/GBAA1542/BAS1430

X: Cellulose Synthase Subunit B a/b domain

X: Core protein P7

X: Type III R-M system modification subunit C-terminal domain

X: Restriction endonuclease-like

X: ClpP/crotonase

X: The "swivelling" beta/beta/alpha domains

X: Barstar (barnase inhibitor)

X: Ribosomal protein L13/L15p/L18e/L32e

X: C-terminal subdomain in Lon-related proteases catalytic domains

X: Atg7 N-terminal domain-like

X: MurF and HprK N-domain-like

X: DTD-like

X: Cell-division inhibitor MinC, N-terminal domain

X: CRISPR-associated Csx3

X: SpoIIaa-like

X: Small protrusion domain in cytoplasmic polyhedrosis virus capsid shell protein

X: Polycomb protein Eed insertion domain

X: HSP90 C-terminal a/b domain

X: STING C-terminal domain

X: C-terminal domain of poxin

X: Glycerate kinase I (Pfam 02595) domain II

X: Dihydrofolate reductases

X: Anticodon-binding domain of Class II aaRS

X: TolB, N-terminal domain

X: ITPase-like

X: Kinesin-like protein KIF23 C-terminal domain

X: N-terminal domain of GerK3 germinant receptor

X: Glutaminase/Asparaginase C-terminal domain

X: O-glucosyltransferase rumi N-terminal domain

X: NIF3 (NGG1p interacting factor 3)-like

X: Isocitrate/Isopropylmalate dehydrogenase-like

X: Single-stranded-DNA-specific exonuclease RecJ C-terminal domain

X: UDP-Glycosyltransferase/glycogen phosphorylase

X: CofD-like

X: Ferredoxin reductase-like, C-terminal NADP-linked domain

X: Alkaline phosphatase-like

X: Nucleotide-diphospho-sugar transferases

X: Nucleoside hydrolase

X: PK C-terminal domain-like

X: ATP synthase (F1-ATPase), gamma subunit

X: CinA-like

X: B12-dependent dehydratase associated subunit

X: TK C-terminal domain-like

X: Periplasmic binding protein-like II

X: ALDH-like

X: Phosphoglycerate mutase-like

X: Initiation factor IF2/eIF5b, domain 3

X: SurE-like/CoA-transferase family III (CaiB/BaiF)

X: Phosphoglucomutase, first 3 domains

X: Macro domain-like

X: Replicase polyprotein 1a N-terminal macro-like domain

X: Carbamate kinase-like

X: Phosphoglycerate kinase domain 1

X: Phosphoglycerate kinase domain 2

X: Undecaprenyl diphosphate synthase

X: Dipeptide transport protein

X: GckA/TtuD-like domain 1

X: PTS IIb component

X: Hypothetical protein MT938 (MTH938)

X: Creatininase

X: Bacterial fluorinating enzyme, N-terminal domain

X: Molybdenum cofactor biosynthesis proteins

X: Aconitase iron-sulfur domain

X: Methylglyoxal synthase-like

X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

X: YchN-like

X: Glutaminase/Asparaginase N-terminal domain

X: Hypothetical protein TT1679

X: Methylesterase CheB, C-terminal domain

X: Indigoidine synthase A-like (Pfam 04227)

X: Tetrapyrrole methylase N-terminal domain

X: ComB-like

X: Amidase signature (AS) enzymes

X: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

X: 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain

X: Alpha-2,3/8-sialyltransferase CstII-related

X: Fe-only hydrogenase

X: DNA polymerase III psi subunit

X: Glycerol-3-phosphate (1)-acyltransferase

X: Ribosomal protein L4

X: Ribose/Galactose isomerase RpiB/AlsB

X: Isochorismatase-like hydrolases

X: Thiamin pyrophosphokinase, catalytic domain

X: MCP/YpsA-related

X: Homo-oligomeric flavin-containing Cys decarboxylases, HFCD

X: Resolvase-like

X: HflX family GTPase N-terminal domain

X: LmbE-like

X: BRCT domain

X: Uracil-DNA glycosylase-like

X: MurD-like peptide ligases, peptide-binding domain

X: Formyltransferase

X: Phosphofructokinase C-terminal domain

X: PRTase-like

X: Thiamin diphosphate-binding fold (THDP-binding)

X: Caspase-like

X: Gingipain R extra N-terminal alpha/beta domain

X: PLP-dependent transferases

X: PhnH-like

X: alpha/beta-Hydrolases

X: RibA-like

X: Thiolase-like

X: Rossmann-like domain in CbiD

X: Rossmann-like domain in AF1104-like proteins

X: Rossmann-like domain in Acetyl-CoA synthetase-like proteins

X: Rossmann-like domains in Sec1/munc18-like proteins

X: Rossmann-like domain in prismane-like proteins

X: Rossmann-like domain in carbohydrate phosphatases

X: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase

X: YgbK-like

X: Middle domain in Argonaute homologs

X: Tetraacyldisaccharide 4'-kinase C-terminal domain

X: CARF (CRISPR-associated Rossmann fold) domains

X: Peroxisome assembly protein 22

X: Hydrogenase expression/formation protein HypD

X: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit

X: GT-D type glycosyltransferase

X: Endolysin C-terminal domain

X: Resistance protein Tm-1 first domain

X: UPF0246 protein YaaA

X: Chromo domain-containing protein 1 (Chp1) domain II

X: Lactate racemase N-terminal domain

X: Lactate racemase C-terminal domain

X: Immunomodulating metalloprotease IMPa N-terminal domain

X: a/b domain in Acetophenone carboxylase (Apc) alpha subunit

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

special