MolNFT v1 · #88897 · protein

Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis in space group P212121 at pH 5.6

4D8Y · Purine nucleoside phosphorylase deod-type: “Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis in space group…”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.82). MolNFT…

PDB: 4D8Y
Type: protein
Length: 1,440 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase deod-type
EC: 2.4.2.1
UniProt: O34925
Ligands: SO4
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Purine nucleoside phosphorylase deod-type (EC 2.4.2.1)	protein	240	35% helix, 28% strand	O34925

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, D, B, C, E, F
GOL · Glycerol · additive · 13 copies · chains A, D, B, C, E, F

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

Pockets

12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1027	0.82	0.83	124	SO4
2	508	0.77	0.84	48	SO4
3	526	0.76	0.84	58	SO4
4	531	0.76	0.84	50	SO4
5	491	0.76	0.84	54	SO4

Interfaces

12 interfaces between chains.

E–F · 2296 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 2289 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 2249 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1785 Å² buried · 25 hydrogen bonds · protein-protein
C–E · 1775 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

4D8Y · Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis… · the same entry in another collection · chain F against F, TM-score 1.00
O34925 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (O34925) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 O34925
Elsewhere: RCSB PDB 4D8Y · PDBe 4D8Y · UniProt O34925

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