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: Tautomerase/MIF-like

X: Uncharacterized protein BTH I2711

X: Peptidase inhibitors family I69

X: Asparaginal-tRNA synthetase N-terminal domain

X: Flagellar hook protein FlgE D0 domain

X: Curli production assembly/transport component CsgF

X: Anti-LPS factor/recA domain

X: Obg GTP-binding protein C-terminal domain-like

X: Ribosomal protein L9 C-domain

X: Urease, gamma-subunit

X: C-terminal domain of nonstructural protein nsp4

X: Putative heterocyst differentiation inhibitor NpR1517

X: Head-to-tail joining protein W, gpW

X: XkdW-like

X: Hypothetical protein MTH677

X: GTF2I-like repeat

X: Ribosomal protein L35p

X: Archaea-specific ribosomal protein L46a

X: PB2 C-terminal domain-like

X: Peptidoglycan deacetylase N-terminal noncatalytic region

X: ERH-like

X: ssDNA binding protein VirE2

X: N-terminal a+b domain in urocanase (Pfam 01175)

X: CbiD-like (Pfam 01888) N-terminal domain

X: Prion-like

X: gp120 inner domain

X: Ribosomal protein L31e-like

X: SSHS domain

X: MTH1598-like

X: Reverse ferredoxin

X: Tetrapyrrole methylase C-terminal domain-like

X: ImmE5-like

X: Polycystin-mucolipin domain

X: UvrB-binding domain of UvrA

X: FAM3 superfamily

X: a+b domain in Ribosomal protein L1

X: Photosystem I subunit PsaD

X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase

X: uncharacterized protein YP_926445.1

X: Insertion domain in phosphocholine transferase AnkX

X: HPr-like

X: EcoKMcrA modification binding domain

X: Allophycocyanin linker chain (domain)

X: Small outer capsid protein (Soc)

X: GYF/BRK domain-like

X: Pesticin N-terminal domain

X: Uncharacterized protein Q2S0R5

X: Tombusvirus P19 core protein, VP19

X: YjbQ-like (Pfam 01894)

X: SSo0622-like (Pfam 02676)

X: MTHFR SAM-binding regulatory domain

X: barrel domain in D-aminoacid aminotransferase-like PLP-dependent enzymes

X: Uncharacterized protein yibL

X: L9 N-domain-like

X: NosL/MerB-like

X: DUF2233 N-terminal domain

X: DNA helicase UvsW N-terminal a+b domain-related

X: EKC/KEOPS complex subunit GON7

X: Putative acetamidase tm0119 C-terminal domain

X: Csm1 ferredoxin-like domain

X: Uncharacterized protein VC_0899

X: ferredoxin-like domain in VP1

X: Seb1 domain 2

X: protein PCC1

X: HLTF protein HIRAN domain

X: Cof C2 cap domain

X: N-terminal domain of vibrio phospholipase

X: Alpha-beta plaits

X: DNA Mimic Protein Arn

X: Ribosomal protein L22e

X: 60S ribosomal export protein NMD3 a+b domain

X: uncharacterized protein lpg1496 N-terminal domain

X: ferredoxin-like domain in flagellar biosynthesis protein flhA

X: Uncharacterized protein VC_A0919

X: PHP14-like

X: N-terminal domain of chitin biosynthesis protein CHS6

X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit

X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit

X: Translation initiation factor eIF4e and phosphothreonine lyase

X: uncharacterized protein SAMEA2273162_06031

X: Ribosomal protein L30p/L7e

X: Insertion domain in 60S ribosomal protein rpP0 (L10P)

X: a+b domain in PB2

X: tRNA pseudouridine synthase TruD insertion domain

X: Barrel domain in dedicator of cytokinesis protein 9

X: YcgL/NE1680-like

X: L,D-transpeptidase C-terminal domain

X: Oxalate Biosynthetic Component A (ObcA) insertion domains

X: GP2-like

X: SdbC C-terminal domain

X: Formate dehydrogenase/DMSO reductase, domain 1

X: 4Fe-4S ferredoxin

X: Diedel

X: Uncharacterized protein MXAN_0049

X: LuxS, MPP, ThrRS/AlaRS common domain

looks like an elaborated ferredoxin

X: Glutamine synthetase-like

X: Cytoplasmic domain of BfpC

X: Ribosomal protein L5

X: hypothetical protein TA0743

X: DCoH-like

X: Prokaryotic AspRS, insert domain

X: Thymidylate synthase-complementing protein Thy1

X: Chorismate synthase, AroC

X: a+b domain in type II DNA topoisomerase

X: TRCF domain

X: Homing endonucleases-like

X: Endonuclease PI-TkoII domain IV

X: C-terminal domain in some PLP-dependent transferases

H: C-terminal domain in some PLP-dependent transferases

T: C-terminal domain in some PLP-dependent transferases

F: GcvP2_C

F: KYNU_C

F: Cys_Met_Meta_PP

F: YhfS-like_C

F: SelA

F: GDC-P

F: Aminotran_1_2

F: Alliinase_C

F: UPF0425_C

F: OKR_DC_1

F: Beta_elim_lyase

F: DegT_DnrJ_EryC1

F: SHMT

F: Pyridoxal_deC

F: Aminotran_5

Representatives:

e1t3iA1[A:305-414] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROBABLE CYSTEINE DESULFURASE ; ligands: 2OS,GOL ; X-RAY DIFFRACTION 1.8Å

e1eg5A1[A:259-376] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å

e4ixoB2[B:252-372] Image Pymol Jmol Links: PDB, SCOP, CATH

NIFS-LIKE PROTEIN ; ligands: CA ; X-RAY DIFFRACTION 2.2Å

e3gzcA3[A:317-444] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; X-RAY DIFFRACTION 2.1Å

e3a9xA3[A:305-373,A:393-432] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; X-RAY DIFFRACTION 2.0Å

e1ecxA2[A:259-376] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE ; ligands: CYS ; X-RAY DIFFRACTION 2.70Å

e1ecxB2[B:259-376] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE ; ligands: CYS ; X-RAY DIFFRACTION 2.70Å

e3vaxA3[A:263-359] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative uncharacterized protein dndA ; X-RAY DIFFRACTION 2.400Å

e3a9yB3[B:305-432] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: CYS ; X-RAY DIFFRACTION 1.85Å

e4hvkA2[A:255-378] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable cysteine desulfurase 2 ; ligands: PG4 ; X-RAY DIFFRACTION 1.43Å

e1p3wB3[B:264-392] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 2.1Å

e3gzcB3[B:317-443] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; X-RAY DIFFRACTION 2.1Å

e3gzdB3[B:317-443] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: NO3 ; X-RAY DIFFRACTION 1.8Å

e3caiA3[A:294-398] Image Pymol Jmol Links: PDB, SCOP, CATH

POSSIBLE AMINOTRANSFERASE ; X-RAY DIFFRACTION 1.8Å

e4eb5A2[A:255-380] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable cysteine desulfurase 2 ; ligands: FES ; X-RAY DIFFRACTION 2.53Å

e3gzdD3[D:317-443] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: NO3 ; X-RAY DIFFRACTION 1.8Å

e3gzdA3[A:317-443] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: NO3 ; X-RAY DIFFRACTION 1.8Å

e4eb7A2[A:255-380] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable cysteine desulfurase 2 ; ligands: FES ; X-RAY DIFFRACTION 2.75Å

e3a9xB3[B:305-429] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: PO4 ; X-RAY DIFFRACTION 2.0Å

e4eb5B2[B:255-378] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable cysteine desulfurase 2 ; ligands: FES ; X-RAY DIFFRACTION 2.53Å

e4eb7B2[B:255-378] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable cysteine desulfurase 2 ; X-RAY DIFFRACTION 2.75Å

e3a9zA3[A:305-432] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: PO4,SLP ; X-RAY DIFFRACTION 1.55Å

e4ixoA2[A:252-369] Image Pymol Jmol Links: PDB, SCOP, CATH

NIFS-LIKE PROTEIN ; X-RAY DIFFRACTION 2.2Å

e3a9zB3[B:305-432] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: SLP ; X-RAY DIFFRACTION 1.55Å

e3gzdC3[C:317-443] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: NO3 ; X-RAY DIFFRACTION 1.8Å

e1eg5B2[B:259-376] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMINOTRANSFERASE ; ligands: SO4 ; X-RAY DIFFRACTION 2.0Å

e3lvmA3[A:264-398] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 2.050Å

e3a9yA3[A:305-432] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SELENOCYSTEINE LYASE ; ligands: CYS,GOL,PO4 ; X-RAY DIFFRACTION 1.85Å

e3vaxB2[B:263-359] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative uncharacterized protein dndA ; X-RAY DIFFRACTION 2.400Å

e3lvjB3[B:264-392] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 2.435Å

e5usrG2[G:316-366,G:403-440] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase, mitochondrial ; X-RAY DIFFRACTION 3.090Å

e3lvlB3[B:264-393] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 3.000Å

e3lvmB3[B:264-393] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 2.050Å

e5usrE2[E:316-359,E:402-436] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase, mitochondrial ; X-RAY DIFFRACTION 3.090Å

e4isyC3[C:261-390] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CYSTEINE DESULFURASE ; X-RAY DIFFRACTION 2.59Å

e5wgbA1[A:316-359,A:404-431] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase, mitochondrial ; X-RAY DIFFRACTION 2.75Å

e3lvjA3[A:264-390] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 2.435Å

e3lvkA3[A:264-392] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Cysteine desulfurase ; X-RAY DIFFRACTION 2.442Å

e4isyA2[A:261-387] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CYSTEINE DESULFURASE ; ligands: GOL ; X-RAY DIFFRACTION 2.59Å

e4isyB2[B:261-386] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CYSTEINE DESULFURASE ; X-RAY DIFFRACTION 2.59Å

e4isyD2[D:261-389] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CYSTEINE DESULFURASE ; X-RAY DIFFRACTION 2.59Å

e3caiB2[B:294-398] Image Pymol Jmol Links: PDB, SCOP, CATH

POSSIBLE AMINOTRANSFERASE ; X-RAY DIFFRACTION 1.8Å

e5kz512[1:316-457] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI