MolNFT v1 · #81320 · protein

Bacillus cereus phosphopentomutase T85E variant

3UN5: “Bacillus cereus phosphopentomutase T85E variant”. X-ray diffraction, 1 ligand (MN), 13 pockets (best druggability 0.76). MolNFT v1 #81320 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3UN5
Type: protein
Length: 2,341 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphopentomutase
EC: 5.4.2.7
UniProt: Q818Z9
Ligands: MN
Pockets: 13 · best druggability 0.76

Structure

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

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

Ligands and binding sites

MN · Manganese (II) ion · metal · 18 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 4 copies · chains A, C, D, F

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1001	0.76	0.79	86	empty
2	831	0.74	0.79	66	empty
3	416	0.68	0.80	39	empty
4	518	0.67	0.78	42	empty
5	504	0.65	0.77	49	empty

Interfaces

6 interfaces between chains.

D–E · 904 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 603 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 373 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 131 Å² buried · 1 hydrogen bond · protein-protein
E–F · 40 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3UN5 · Bacillus cereus phosphopentomutase T85E variant · the same entry in another collection · chain D against D, 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 3UN5 · PDBe 3UN5 · UniProt Q818Z9

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