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

H: Alkaline phosphatase-like

T: Alkaline phosphatase-like

F: SGSH_C

PF16347 CL0088

F: Metalloenzyme

PF01676 CL0088

Representatives:

e1o98A1[A:2-76,A:311-510] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE ; ligands: 2PG,MN,SO4 ; X-RAY DIFFRACTION 1.4Å

e1ejjA1[A:3-76,A:311-510] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PHOSPHOGLYCERATE MUTASE ; ligands: 3PG,MN ; X-RAY DIFFRACTION 1.9Å

e1eqjA3[A:3-76,A:311-510] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PHOSPHOGLYCERATE MUTASE ; ligands: 2PG,MN ; X-RAY DIFFRACTION 1.7Å

e2ifyA3[A:2-75,A:310-509] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN ; X-RAY DIFFRACTION 2.38Å

e3igyB2[B:4-89,B:332-552] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cofactor-independent phosphoglycerate mutase ; ligands: 2PG,3PG,CO,NA ; X-RAY DIFFRACTION 2.00Å

e3igzB3[B:4-89,B:332-552] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cofactor-independent phosphoglycerate mutase ; ligands: 2PG,3PG,CO,NA ; X-RAY DIFFRACTION 1.900Å

e4my4A1[A:3-76,A:305-505] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN ; X-RAY DIFFRACTION 2.00Å

e4nwxA2[A:3-76,A:305-505] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: DTT,MN ; X-RAY DIFFRACTION 2.01Å

e1o99A1[A:2-76,A:311-511] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE ; ligands: 2PG,MN,SO4 ; X-RAY DIFFRACTION 2.65Å

e4qaxA2[A:3-76,A:305-505] Image Pymol Jmol Links: PDB, SCOP, CATH

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN ; X-RAY DIFFRACTION 2.00Å

e3nvlB1[B:3-88,B:331-551] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: CO ; X-RAY DIFFRACTION 2.300Å

e5kglA1[A:20-100,A:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN,SO4,ZN ; X-RAY DIFFRACTION 2.450Å

e5kglB2[B:20-100,B:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN,SO4,ZN ; X-RAY DIFFRACTION 2.450Å

e5kgmA1[A:20-100,A:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: CL,MN,ZN ; X-RAY DIFFRACTION 2.950Å

e5kgmB1[B:20-100,B:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: CL,MN,ZN ; X-RAY DIFFRACTION 2.950Å

e5kgnA2[A:20-100,A:334-549] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: CL,MG,MN,ZN ; X-RAY DIFFRACTION 1.950Å

e5kgnB2[B:19-100,B:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: CL,MG,MN,ZN ; X-RAY DIFFRACTION 1.950Å

e5vpuA2[A:6-81,A:311-514] Image Pymol Jmol Links: PDB, SCOP, CATH

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: 3PG,ACT,EDO,MN ; X-RAY DIFFRACTION 1.500Å

e4nwjA3[A:2-76,A:295-505] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN ; X-RAY DIFFRACTION 2.01Å

e7kngB1[B:20-100,B:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: NA,ZN ; X-RAY DIFFRACTION 2.100Å

e7kngA2[A:20-100,A:334-538] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: NA,ZN ; X-RAY DIFFRACTION 2.100Å

e7knfA2[A:27-100,A:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: HOA,NA,PG4,ZN ; X-RAY DIFFRACTION 1.800Å

e7knfB1[B:27-100,B:334-539] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: HOA,NA,PG4,ZN ; X-RAY DIFFRACTION 1.800Å

e7tl7A2[A:19-100,A:334-549] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: IMD,NA,ZN ; X-RAY DIFFRACTION 1.900Å

e7tl7B2[B:19-100,B:334-544] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: IMD,NA,ZN ; X-RAY DIFFRACTION 1.900Å

e7tl7C1[C:20-100,C:334-541] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: IMD,NA,ZN ; X-RAY DIFFRACTION 1.900Å

e7tl7D1[D:20-100,D:334-540] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: IMD,NA,ZN ; X-RAY DIFFRACTION 1.900Å

e7tl8A2[A:1-76,A:295-505] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

2,3-bisphosphoglycerate-independent phosphoglycerate mutase ; ligands: MN ; X-RAY DIFFRACTION 1.950Å

e3m7vA1[A:3-107,A:227-403] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

Phosphopentomutase ; ligands: GOL,MN ; X-RAY DIFFRACTION 2.0Å

e3iddA1[A:3-88,A:230-397] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE ; X-RAY DIFFRACTION 2.8Å

F: Alk_phosphatase

F: Phosphoesterase

F: Sulfatase

F: Phosphodiest

F: Phosphodiest,SGSH_C

PF01663 PF16347

F: Sulfatase,SGSH_C

PF00884 PF16347

F: Sulfatase,Sulfatase_C

PF00884 PF14707

F: Sulfatase,Choline_sulf_C

PF00884 PF12411

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