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

X: SRF-like

X: Fe,Mn superoxide dismutase (SOD)-C

X: Nigritoxin middle domain

X: Mitochondrial complex I, B17.2 subunit

X: Gelsolin-like

X: GIY-YIG endonuclease

X: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1

X: Regulatory factor Nef

X: Hut operon positive regulatory protein HutP

X: Mitochondrial homologous recombination protein 1

X: Nucleotidyltransferase-like

X: N-terminal a+b domain in adenylylcyclase toxin

X: a+b domain in Rap/Ran-GAP (Pfam 02145)

X: C-terminal segment in 5'->3' exoribonucleases

X: Profilin-like

X: Sensor domain of histidine kinase VC_A0565

X: Nonstructural protein V

X: Putative sensor histidine kinase domain

X: a+b domain in antivirulence factor

X: HIT-like

X: DUF1827-like

X: PR-1-like

X: L-sulfolactate dehydrogenase-like

X: AraD-like aldolase/epimerase

X: N-acetylmuramoyl-L-alanine amidase-like

X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4

X: Cryptic loci regulator 2 N-terminal domain

X: thylakoid acid phosphatase domain-related

X: Thioredoxin-like

X: Thioredoxin-like domain in RNase E

X: Major capsid protein GP7

X: Bacillus chorismate mutase-like

H: L30e-like

H: PurM N-terminal domain-like

H: OmpA-like

H: YueI-like

H: BB2672-like

H: Holliday junction resolvase RusA

H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF

H: Tubulin C-terminal domain-like

H: Conserved hypothetical protein in Lin0512 family

H: YjgF-like

H: 4'-phosphopantetheinyl transferase

H: HypA Ni-binding domain

T: HypA Ni-binding domain

F: HypA

PF01155

Representatives:

e5aunA2[A:1-68,A:124-136] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; ligands: CL,GOL,NI,URE ; X-RAY DIFFRACTION 1.630Å

e3a43A2[A:1-68,A:124-139] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase nickel incorporation protein hypA ; X-RAY DIFFRACTION 2.3Å

e3a44B3[B:1-68,B:124-136] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase nickel incorporation protein hypA ; X-RAY DIFFRACTION 3.3Å

e3a44C3[C:2-68,C:124-137] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase nickel incorporation protein hypA ; X-RAY DIFFRACTION 3.3Å

e3a44D2[D:3-68,D:124-137] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase nickel incorporation protein hypA ; X-RAY DIFFRACTION 3.3Å

e5auoA1[A:1-68,A:124-136] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; ligands: CL,NI ; X-RAY DIFFRACTION 1.80Å

e5aupA1[A:1-68,A:124-136] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; X-RAY DIFFRACTION 3.10Å

e5aupH2[H:1-68,H:124-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; X-RAY DIFFRACTION 3.10Å

e3a43B1[B:1-86,B:108-139] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase nickel incorporation protein hypA ; ligands: ZN ; X-RAY DIFFRACTION 2.3Å

e3a44A1[A:2-68] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase nickel incorporation protein hypA ; X-RAY DIFFRACTION 3.3Å

e2kdxA1[A:1-119] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase/urease nickel incorporation protein hypA ; ligands: ZN ; SOLUTION NMR

e5yxyE2[E:2-68,E:124-136] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; X-RAY DIFFRACTION 3.299Å

e6g81A1[A:1-117] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Hydrogenase maturation factor HypA ; ligands: ZN ; SOLUTION NMR

e5yxyD2[D:2-68,D:124-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; X-RAY DIFFRACTION 3.299Å

e5yxyF1[F:2-68,F:124-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; X-RAY DIFFRACTION 3.299Å

e5yy0B2[B:2-68,B:124-135] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Probable hydrogenase nickel incorporation protein HypA ; X-RAY DIFFRACTION 3.243Å

H: DAK1/DegV C-terminal domain

X: CofE-like

X: a+b domain in conserved hypothetical protein Rv3899c

X: Cytidine deaminase-like

X: Phospholipase D/nuclease

X: Phoshotransferase/anion transport protein

X: Mid-cell-anchored protein Z (MapZ) extracellular domain 2

X: Class II aaRS and biotin synthetases

X: Protein interacting with HSP90 1 (Pih1) N-terminal domain

X: Suppressor of Fused, N-terminal domain

X: Suppressor of Fused, C-terminal domain

X: Hypothetical protein MTH1880

X: Hypothetical protein Ta1206-like

X: CytB endotoxin-like (Pfam 01338)

X: Coproporphyrinogen III oxidase

X: Mog1p/PsbP-like

X: Two-component system yycF/yycG regulatory protein yycH-like

X: B12-dependent (class II) ribonucleotide reductase, insertion domain

X: CorA soluble domain-like

X: DeoB insert domain-like

X: DisA nucleotide-binding domain

X: Coronavirus spike protein receptor-binding domain

X: C-terminal domain in DHH phosphoesterases

X: PlyCB

X: Surfactant protein C BRICHOS domain

X: Late genes activator p4

X: AF1514-like

X: YehU-like

X: Nat/Ivy

X: Integron cassette protein VCH_CASS3

X: Polymerase basic protein 2 cap-binding domain

X: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

X: ESX-1 secretion system protein eccB1 modular domains

X: Fibrinogen binding protein a+b domain

X: C-terminal domain of N-acetylglucosaminyltransferase-V

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

special