MolNFT v1 · #82775 · protein

Crystal structure of xylobiose-bxle complex from streptomyces thermoviolaceus opc-520

3VXC · Putative sugar-binding lipoprotein: “Crystal structure of xylobiose-bxle complex from streptomyces thermoviolaceus opc-520”. X-ray diffraction, 1 ligand (XYP), 4 pockets (best druggability 0.73). MolNFT v1 #82775 on GenesisL1: 3D…

PDB: 3VXC
Type: protein
Length: 796 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative sugar-binding lipoprotein
UniProt: Q76BU9
Ligands: XYP
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative sugar-binding lipoprotein	protein	398	52% helix, 16% strand	Q76BU9

Ligands and binding sites

XYP · beta-D-xylopyranose · sugar · 4 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.73	0.88	50	XYP
2	338	0.70	0.83	74	XYP
3	686	0.70	0.77	83	empty
4	54	0.25	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 891 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3VXC · Crystal Structure of Xylobiose-BxlE complex from Streptomyces thermoviolaceus OPC-520 · 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 Q76BU9
Elsewhere: RCSB PDB 3VXC · PDBe 3VXC · UniProt Q76BU9

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