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Crystal structure of HddC from Yersinia pseudotuberculosis complexed with GMP-PN

Analyse Crystal structure of HddC from Yersinia pseudotuberculosis complexed with GMP-PN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JQ8
Type: protein
Length: 225 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.546
Source: Yersinia pseudotuberculosis
Molecule: Putative 6-deoxy-D-mannoheptose pathway protein
UniProt: Q8GJ95
Ligands: GNH, MG
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · resolution 1.546 · 1 distinct chain · 27% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative 6-deoxy-D-mannoheptose pathway protein	protein	225	27% helix, 33% strand	Q8GJ95

Ligands and binding sites

GNH · Aminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
CIT · Citric acid · additive · 2 copies · 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	386	0.61	0.77	46	MG, GNH, CIT

Compared structures

6JQ8 · Crystal structure of hddc from yersinia pseudotuberculosis complexed with gmp-pn · 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 Q8GJ95
Elsewhere: RCSB PDB 6JQ8 · PDBe 6JQ8 · UniProt Q8GJ95

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