MolNFT v1 · #129910 · protein

GH5 endo-xyloglucanase from cellvibrio japonicus

5OYE · Cellulase, putative, CEL5D: “GH5 endo-xyloglucanase from cellvibrio japonicus”. X-ray diffraction, 5 ligands (BGC, XYS, GAL), 3 pockets (best druggability 0.71). MolNFT v1 #129910 on GenesisL1: 3D structure, binding sites and…

PDB: 5OYE
Type: protein
Length: 742 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cellulase, putative, CEL5D
EC: 3.2.1.151
UniProt: B3PD52
Ligands: BGC, XYS, GAL, SO4, CL
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cellulase, putative, CEL5D (EC 3.2.1.151)	protein	372	41% helix, 12% strand	B3PD52
B	Cellulase, putative, CEL5D (EC 3.2.1.151)	protein	370	41% helix, 12% strand	B3PD52

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B
XYS · alpha-D-xylopyranose · sugar · 4 copies · chains A, B
GAL · beta-D-galactopyranose · sugar · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
CL · Chloride ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1030	0.71	0.75	87	BGC, XYS, GAL
2	272	0.51	0.74	25	BGC, XYS
3	149	0.49	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 692 Å² buried · 4 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt B3PD52
Elsewhere: RCSB PDB 5OYE · PDBe 5OYE · UniProt B3PD52

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