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X - Possible homology level

H - Homology level

T - Topology level

F - Family level

* - Provisional representative

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Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

X: PGBD-like
H: PGBD-like
T: PGBD-like
F: PG_binding_1

PF01471 CL0244

Representatives:

e4g54A2[A:459-539] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

GENERAL SECRETION PATHWAY PROTEIN ; X-RAY DIFFRACTION 1.55Å

e5nm7G1[G:2-74] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Peptidoglycan-binding domain 1 ; ligands: GLY ; X-RAY DIFFRACTION 1.72Å

e1lbuA1[A:1-83] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH

MURAMOYL-PENTAPEPTIDE CARBOXYPEPTIDASE ; X-RAY DIFFRACTION 1.8Å

e5bmqA2[A:99-173] Image Pymol Jmol Links: PDB, SCOP, CATH

ErfK/YbiS/YcfS/YnhG family protein ; X-RAY DIFFRACTION 2.050Å

e5ao7A2[A:345-420] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SOLUBLE LYTIC TRANSGLYCOSYLASE B3 ; ligands: TRS ; X-RAY DIFFRACTION 1.77Å

e5ao8A2[A:350-419] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SOLUBLE LYTIC TRANGLYCOSILASE B3 ; X-RAY DIFFRACTION 2.23Å

e1slmA1[A:16-80] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

STROMELYSIN-1 ; ligands: ZN ; X-RAY DIFFRACTION 1.90Å

e1su3B2[B:32-98] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INTERSTITIAL COLLAGENASE ; ligands: EPE,ZN ; X-RAY DIFFRACTION 2.2Å

e1eakB1[B:35-107] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 2.650Å

e1ck7A2[A:35-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

PROTEIN (GELATINASE A) ; ligands: SO4,ZN ; X-RAY DIFFRACTION 2.8Å

e1eakD1[D:35-107] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 2.650Å

e1eakC1[C:35-107] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 2.650Å

e1gxdB2[B:6-78] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 3.100Å

e1eakA1[A:35-107] Image Pymol Jmol Links: PDB, SCOP, CATH

72 KDA TYPE IV COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 2.650Å

e4bj4B1[B:182-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPDH2 ; X-RAY DIFFRACTION 1.72Å

e4lpqA2[A:123-197] Image Pymol Jmol Links: PDB, SCOP, CATH

ERFK/YBIS/YCFS/YNHG FAMILY PROTEIN ; ligands: CL ; X-RAY DIFFRACTION 1.37Å

e3bkhA3[A:-7-71] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LYTIC TRANSGLYCOSYLASE ; ligands: NI,SO4 ; X-RAY DIFFRACTION 2.5Å

e4c2eA15[A:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 1.8Å

e4bj4A6[A:183-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPDH2 ; X-RAY DIFFRACTION 1.72Å

e3bkvA3[A:-7-71] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

LYTIC TRANSGLYCOSYLASE ; ligands: NI,SO4 ; X-RAY DIFFRACTION 2.6Å

e4c2dD2[D:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 2.7Å

e4c2cA2[A:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 1.9Å

e4c2dA2[A:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 2.7Å

e4c2dB2[B:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 2.7Å

e4c2dC2[C:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 2.7Å

e4c2eB2[B:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 1.8Å

e4c2fA2[A:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 2.4Å

e4c2gA2[A:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 1.90Å

e4c2hA2[A:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 1.95Å

e4c2hB2[B:383-479] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

CARBOXY-TERMINAL PROCESSING PROTEASE CTPB ; X-RAY DIFFRACTION 1.95Å

e4bpaA2[A:183-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPDH2 ; X-RAY DIFFRACTION 2.7Å

e4bolA2[A:182-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPDH2 ; X-RAY DIFFRACTION 1.7Å

e4bolB2[B:182-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPDH2 ; X-RAY DIFFRACTION 1.7Å

e4bpaB2[B:182-259] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

AMPDH2 ; X-RAY DIFFRACTION 2.7Å

e1gxdA4[A:1-80] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

72 KDA TYPE IV COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 3.100Å

e4xxtA1[A:53-128] Image Pymol Jmol Links: PDB, SCOP, CATH

Fusion of predicted Zn-dependent amidase/peptidase (Cell wall hydrolase/DD-carboxypeptidase family) and uncharacterized domain of ErfK family peptodoglycan-binding domain ; ligands: ACT,EDO,IMD ; X-RAY DIFFRACTION 1.770Å

e2mzeA2[A:-2-74] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrilysin ; ligands: ZN ; SOLUTION NMR

e2mzhA1[A:0-74] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrilysin ; ligands: ZN ; SOLUTION NMR

e5anzA2[A:349-420] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

SOLUBLE LYTIC TRANSGLYCOSYLASE B3 ; X-RAY DIFFRACTION 1.61Å

e2mziA2[A:0-74] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrilysin ; ligands: ZN ; SOLUTION NMR

e5tv7A1[A:126-200] Image Pymol Jmol Links: PDB, SCOP, CATH

Putative peptidoglycan-binding/hydrolysing protein ; ligands: HGA ; X-RAY DIFFRACTION 2.05Å

e5ue2A1[A:1-74] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrilysin ; ligands: IDS,SGN,ZN ; SOLUTION NMR

e5ue5A2[A:1-74] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrilysin ; ligands: ZN ; SOLUTION NMR

e6tciA1[A:124-196] Image Pymol Jmol Links: PDB, SCOP, CATH

Spore cortex-lytic enzyme ; X-RAY DIFFRACTION 1.47Å

e7kgmA3[A:236-287,A:323-377] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Putative exported protein ; X-RAY DIFFRACTION 2.6Å

e7kgnA2[A:215-266,A:312-366] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

L,D-transpeptidase ; X-RAY DIFFRACTION 2.200Å

e7aj9A1[A:169-284] Image Pymol Jmol Links: PDB, SCOP, CATH

L,D-transpeptidase YcbB ; ligands: EDO ; X-RAY DIFFRACTION 2.35Å

e7aj9B3[B:169-284] Image Pymol Jmol Links: PDB, SCOP, CATH

L,D-transpeptidase YcbB ; ligands: EDO ; X-RAY DIFFRACTION 2.35Å

e7ajoA3[A:169-284] Image Pymol Jmol Links: PDB, SCOP, CATH

L,D-transpeptidase YcbB ; ligands: EDO ; X-RAY DIFFRACTION 1.85Å

e7ajxA2[A:169-284] Image Pymol Jmol Links: PDB, SCOP, CATH

L,D-transpeptidase YcbB ; ligands: EDO ; X-RAY DIFFRACTION 2.55Å

e7ajzA2[A:169-284] Image Pymol Jmol Links: PDB, SCOP, CATH

L,D-transpeptidase YcbB ; X-RAY DIFFRACTION 2.98Å

e7ajzB2[B:169-284] Image Pymol Jmol Links: PDB, SCOP, CATH

L,D-transpeptidase YcbB ; ligands: EDO ; X-RAY DIFFRACTION 2.98Å

e7qvdAAA1[AAA:324-398] Image Pymol Jmol Links: PDB, SCOP, CATH

; X-RAY DIFFRACTION 1.70Å

e5th6A2[A:41-58,A:61-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 1.700Å

e5th6B2[B:42-58,B:61-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 1.700Å

e5th6C1[C:40-58,C:61-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 1.700Å

e5th6D1[D:40-58,D:61-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 1.700Å

e5th9A1[A:40-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 3.000Å

e5th9B2[B:40-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 3.000Å

e5th9C2[C:41-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9,Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 3.000Å

e5ue3A2[A:41-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 1.599Å

e5ue3B2[B:41-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9 ; ligands: SO4,ZN ; X-RAY DIFFRACTION 1.599Å

e5ue4A2[A:40-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9 ; ligands: ZN ; X-RAY DIFFRACTION 1.8Å

e5ue4B2[B:41-107] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

Matrix metalloproteinase-9 ; ligands: 5XQ,ZN ; X-RAY DIFFRACTION 1.8Å

e1su3A2[A:32-98] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

INTERSTITIAL COLLAGENASE ; ligands: ZN ; X-RAY DIFFRACTION 2.2Å

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.

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

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