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

Analyse Crystal structure of the hexameric purine nucleoside phosphorylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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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