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Open liganded crystal structure of xylose binding protein from Escherichia coli

Analyse Open liganded crystal structure of xylose binding protein from Escherichia coli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M9X
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Escherichia coli
Molecule: D-xylose-binding periplasmic protein
UniProt: P37387
Ligands: XYP
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · resolution 2.2 · 1 distinct chain · 43% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-xylose-binding periplasmic protein	protein	305	43% helix, 21% strand	P37387

Ligands and binding sites

XYP · beta-D-xylopyranose · sugar · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	423	0.60	0.76	47	XYP

Compared structures

3M9X · Open liganded crystal structure of xylose binding protein from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
P37387 · AlphaFold monomer V2.0 prediction for D-xylose-binding periplasmic protein (P37387) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 P37387
Elsewhere: RCSB PDB 3M9X · PDBe 3M9X · UniProt P37387

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