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

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

H: PLP-dependent transferases

T: PLP-dependent transferases

F: Asp_aminotransf

F: Met_gamma_lyase

F: OKR_DC_1

F: Beta_elim_lyase

F: SepSecS

F: SelA

F: GDC-P

F: Aminotran_1_2

F: SHMT

F: Aminotran_3

F: Alliinase_C

F: Pyridoxal_deC

Representatives:

e1pmmA2[A:3-336] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GLUTAMATE DECARBOXYLASE BETA ; ligands: ACY,PLP ; X-RAY DIFFRACTION 2.0Å

e1js3A2[A:1-371] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

DOPA DECARBOXYLASE ; ligands: 142,PLP,SO4 ; X-RAY DIFFRACTION 2.25Å

e6zekD1[D:14-374] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine sulfinic acid decarboxylase ; ligands: CL,GOL ; X-RAY DIFFRACTION 2.10Å

e7a0aC1[C:12-374] Image Pymol Jmol Links: PDB, SCOP, CATH

Cysteine sulfinic acid decarboxylase ; ligands: SO4 ; X-RAY DIFFRACTION 2.80Å

e7a0aA1[A:13-374] Image Pymol Jmol Links: PDB, SCOP, CATH

Cysteine sulfinic acid decarboxylase ; ligands: SO4 ; X-RAY DIFFRACTION 2.80Å

e7a0aB1[B:13-374] Image Pymol Jmol Links: PDB, SCOP, CATH

Cysteine sulfinic acid decarboxylase ; X-RAY DIFFRACTION 2.80Å

e7a0aD1[D:14-374] Image Pymol Jmol Links: PDB, SCOP, CATH

Cysteine sulfinic acid decarboxylase ; X-RAY DIFFRACTION 2.80Å

e7cwxA1[A:8-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: PEG ; X-RAY DIFFRACTION 2.150Å

e7cwxB1[B:6-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: GOL,PEG ; X-RAY DIFFRACTION 2.150Å

e7cwxC1[C:5-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: GOL,PEG ; X-RAY DIFFRACTION 2.150Å

e7cwyA1[A:8-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; X-RAY DIFFRACTION 2.590Å

e7cwyB1[B:6-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; X-RAY DIFFRACTION 2.590Å

e7cwyC1[C:6-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; X-RAY DIFFRACTION 2.590Å

e7cwzA2[A:8-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: LDP,PLP ; X-RAY DIFFRACTION 2.970Å

e7cwzB1[B:6-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: LDP,PLP ; X-RAY DIFFRACTION 2.970Å

e7cwzC1[C:4-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: LDP,PLP ; X-RAY DIFFRACTION 2.970Å

e7cx0A1[A:8-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: 142,PLP ; X-RAY DIFFRACTION 2.660Å

e7cx0B2[B:6-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: 142,PLP ; X-RAY DIFFRACTION 2.660Å

e7cx0C2[C:4-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: 142,PLP ; X-RAY DIFFRACTION 2.660Å

e7cx1A1[A:8-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: GKU ; X-RAY DIFFRACTION 2.54Å

e7cx1B2[B:6-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: GKU ; X-RAY DIFFRACTION 2.54Å

e7cx1C1[C:5-464] Image Pymol Jmol Links: PDB, SCOP, CATH

Decarboxylase ; ligands: GKU ; X-RAY DIFFRACTION 2.54Å

e7eiwA2[A:2-359] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Histidine decarboxylase ; ligands: PLP ; X-RAY DIFFRACTION 2.10Å

e7eiwB2[B:1-359] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Histidine decarboxylase ; ligands: PLP ; X-RAY DIFFRACTION 2.10Å

e7eixA1[A:2-359] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Histidine decarboxylase ; ligands: PLP,SO4 ; X-RAY DIFFRACTION 1.9Å

e7eixB2[B:1-359] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Histidine decarboxylase ; ligands: PLP,SO4 ; X-RAY DIFFRACTION 1.9Å

e7eiyA1[A:2-359] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Histidine decarboxylase ; ligands: HIS,PLP,SO4 ; X-RAY DIFFRACTION 2.2Å

e7eiyB1[B:1-359] Image Pymol Jmol Links: PDB, SCOP, CATH DOI

Histidine decarboxylase ; ligands: HIS,PLP,SO4 ; X-RAY DIFFRACTION 2.2Å

e7x4lA1[A:25-334] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI