Research workbench

Xanthomonas citri phospho-pgm in complex with mannose-6-phosphate

Analyse Xanthomonas citri phospho-pgm in complex with mannose-6-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NP8
Type: protein
Length: 448 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglucomutase
UniProt: Q8PGN7
Ligands: M6P, CA
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglucomutase	protein	448	39% helix, 21% strand	Q8PGN7

Ligands and binding sites

M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · chains A
CA · Calcium ion · metal · chains A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A

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

Pockets

4 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	369	0.72	0.84	49	M6P
2	69	0.34	0.76	14	empty
3	52	0.28	0.75	13	empty
4	50	0.26	0.74	13	empty

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

6NP8 · Xanthomonas citri Phospho-PGM in complex with mannose-6-phosphate · 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 Q8PGN7
Elsewhere: RCSB PDB 6NP8 · PDBe 6NP8 · UniProt Q8PGN7

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