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Phosphopentomutase soaked with 2,3-dideoxyribose 5-phosphate

Analyse Phosphopentomutase soaked with 2,3-dideoxyribose 5-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LRE
Type: protein
Length: 1,172 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: 1X4, MN
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphopentomutase (EC 5.4.2.7)	protein	391	35% helix, 21% strand	Q818Z9
C	Phosphopentomutase (EC 5.4.2.7)	protein	390	34% helix, 21% strand	Q818Z9

Ligands and binding sites

1X4 · 2,3-dideoxy-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A
MN · Manganese (II) ion · metal · 10 copies · chains A, B, C

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

Pockets

4 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	984	0.78	0.80	99	1X4
2	1054	0.73	0.77	71	empty
3	536	0.69	0.79	55	empty
4	447	0.67	0.79	61	empty

Interfaces

2 interfaces between chains.

B–C · 886 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 326 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (phosphorylation).

Compared structures

4LRE · Phosphopentomutase soaked with 2,3-dideoxyribose 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 0.99

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 4LRE · PDBe 4LRE · UniProt Q818Z9

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