MolNFT v1 · #81318 · protein

Phosphopentomutase T85Q variant soaked with glucose 1,6-bisphosphate

3UN3: “Phosphopentomutase T85Q variant soaked with glucose 1,6-bisphosphate”. X-ray diffraction, 2 ligands (G16, MN), 6 pockets (best druggability 0.78). MolNFT v1 #81318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3UN3
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: G16, MN
Pockets: 6 · best druggability 0.78

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	36% helix, 21% strand	Q818Z9

Ligands and binding sites

G16 · 1,6-di-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains A, B, C
MN · Manganese (II) ion · metal · 12 copies · chains A, B, C
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

6 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	991	0.78	0.80	96	G16
2	830	0.73	0.78	64	MN
3	343	0.69	0.83	32	empty
4	300	0.64	0.81	33	empty
5	53	0.29	0.75	11	empty

Interfaces

2 interfaces between chains.

B–C · 892 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 339 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3UN3 · phosphopentomutase T85Q variant soaked with glucose 1,6-bisphosphate · 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 3UN3 · PDBe 3UN3 · UniProt Q818Z9

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