MolNFT v1 · #103653 · protein

Crystal structure of GH10 endo-B-1,4-xylanase (xynb) from xanthomonas axonopodis pv citri complexed with xylotriose

4PN2: “Crystal structure of GH10 endo-B-1,4-xylanase (xynb) from xanthomonas axonopodis pv citri complexed with…”. X-ray diffraction, 2 ligands (XYP, CA), 4 pockets (best druggability 0.46). MolNFT v1 #103653 on GenesisL1: 3D structure…

PDB: 4PN2
Type: protein
Length: 610 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylanase
UniProt: Q8PET6
Ligands: XYP, CA
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xylanase	protein	305	38% helix, 14% strand	Q8PET6

Ligands and binding sites

XYP · beta-D-xylopyranose · sugar · 6 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.46	0.76	28	empty
2	141	0.46	0.77	29	empty
3	61	0.40	0.80	14	empty
4	62	0.37	0.79	15	XYP

Interfaces

1 interface between chains.

A–B · 427 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4PN2 · Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri… · 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 Q8PET6
Elsewhere: RCSB PDB 4PN2 · PDBe 4PN2 · UniProt Q8PET6

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