MolNFT v1 · #54646 · protein

Crystal structure of alpha-xylosidase (GH31) from cellvibrio japonicus

2XVG · Alpha xylosidase: “Crystal structure of alpha-xylosidase (GH31) from cellvibrio japonicus”. X-ray diffraction, 3 ligands (NI, CL, SO4), 9 pockets (best druggability 0.66). MolNFT v1 #54646 on GenesisL1: 3D structure, binding sites…

PDB: 2XVG
Type: protein
Length: 944 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha xylosidase
EC: 3.2.1.-
UniProt: B3PBD9
Ligands: NI, CL, SO4
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha xylosidase (EC 3.2.1.-)	protein	944	21% helix, 32% strand	B3PBD9

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 4 copies · chains A
SO4 · Sulfate ion · ion · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.66	0.90	19	empty
2	120	0.65	0.89	32	empty
3	94	0.63	0.90	28	empty
4	273	0.61	0.79	45	EDO
5	189	0.48	0.76	26	empty

Compared structures

2XVG · crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus · the same entry in another collection · chain A against A, TM-score 1.00

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 B3PBD9
Elsewhere: RCSB PDB 2XVG · PDBe 2XVG · UniProt B3PBD9

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