MolNFT v1 · #99021 · protein

Phosphopentomutase S154A variant soaked with ribose 5-phosphate

4LR8: “Phosphopentomutase S154A variant soaked with ribose 5-phosphate”. X-ray diffraction, 2 ligands (HSX, MN), 7 pockets (best druggability 0.74). MolNFT v1 #99021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4LR8
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: 7 · best druggability 0.74

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, 22% strand	Q818Z9
B, C	Phosphopentomutase (EC 5.4.2.7)	protein	390	36% 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
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	804	0.74	0.79	63	empty
2	646	0.72	0.79	55	empty
3	378	0.68	0.81	44	empty
4	301	0.66	0.82	44	HSX
5	447	0.66	0.79	53	empty

Interfaces

2 interfaces between chains.

B–C · 928 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 365 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 1 covalent (phosphorylation, covalent ligand).

Compared structures

4LR8 · Phosphopentomutase S154A variant soaked 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 4LR8 · PDBe 4LR8 · UniProt Q818Z9

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