MolNFT v1 · #24970 · protein

Crystal structure of native xylanase 10B from thermotoga maritima

1VBU · Endo-1,4-beta-xylanase B: “Crystal structure of native xylanase 10B from thermotoga maritima”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.55). MolNFT v1 #24970 on GenesisL1: 3D structure, binding sites and…

PDB: 1VBU
Type: protein
Length: 648 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-1,4-beta-xylanase B
EC: 3.2.1.8
UniProt: Q9WXS5
Ligands: SO4
Pockets: 3 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Endo-1,4-beta-xylanase B (EC 3.2.1.8)	protein	324	45% helix, 20% strand	Q9WXS5

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, B
ACY · Acetic acid · additive · 6 copies · chains A, B
GOL · Glycerol · additive · 2 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	311	0.55	0.76	40	empty
2	108	0.41	0.76	19	ACY, GOL
3	113	0.39	0.75	29	ACY, GOL

Interfaces

1 interface between chains.

A–B · 488 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1VBU · Crystal structure of native xylanase 10B from Thermotoga maritima · 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 Q9WXS5
Elsewhere: RCSB PDB 1VBU · PDBe 1VBU · UniProt Q9WXS5

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