MolNFT v1 · #161256 · protein

GH10 endo-xylanase

6Q8M · Beta-xylanase: “GH10 endo-xylanase”. X-ray diffraction, 2 ligands (NAG, K), 3 pockets (best druggability 0.59). MolNFT v1 #161256 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Q8M
Type: protein
Length: 642 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-xylanase
EC: 3.2.1.8
UniProt: A0A1L9WG58
Ligands: NAG, K
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-xylanase (EC 3.2.1.8)	protein	321	45% helix, 20% strand	A0A1L9WG58

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
K · Potassium ion · metal · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 35 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	343	0.59	0.77	54	EDO, K
2	138	0.46	0.77	26	EDO, K
3	69	0.31	0.74	20	EDO

Interfaces

1 interface between chains.

A–B · 634 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6Q8M · GH10 endo-xylanase · 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 A0A1L9WG58
Elsewhere: RCSB PDB 6Q8M · PDBe 6Q8M · UniProt A0A1L9WG58

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