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Phosphopentomutase from bacillus cereus bound with ribose-5-phosphate

Analyse Phosphopentomutase from bacillus cereus bound with ribose-5-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M8Z
Type: protein
Length: 1,171 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphopentomutase
EC: 5.4.2.7
UniProt: Q818Z9
Ligands: HSX, MN
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphopentomutase (EC 5.4.2.7)	protein	391	35% helix, 21% strand	Q818Z9
B, C	Phosphopentomutase (EC 5.4.2.7)	protein	390	35% helix, 21% strand	Q818Z9

Ligands and binding sites

HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A
MN · Manganese (II) ion · metal · 9 copies · chains A, B, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1200	0.75	0.78	104	HSX
2	799	0.74	0.79	67	empty
3	448	0.70	0.81	48	empty
4	353	0.67	0.81	43	empty
5	57	0.25	0.73	15	empty

Interfaces

2 interfaces between chains.

B–C · 919 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 358 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 2 covalent (phosphorylation, covalent ligand).

Compared structures

3M8Z · Phosphopentomutase from Bacillus cereus bound with ribose-5-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
Q818Z9 · AlphaFold monomer V2.0 prediction for phosphopentomutase (Q818Z9) · a predicted model of the same protein · 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 Q818Z9
Elsewhere: RCSB PDB 3M8Z · PDBe 3M8Z · UniProt Q818Z9

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