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Crystal structure of human purine nucleoside phosphorylase in complex with datme-immh

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

PDB: 3K8O
Type: protein
Length: 1,699 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Purine nucleoside phosphorylase
EC: 2.4.2.1
UniProt: P00491
Ligands: 229, SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, Y	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	283	34% helix, 24% strand	P00491
Q	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	284	35% helix, 23% strand	P00491
S	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	282	33% helix, 24% strand	P00491
T	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	282	32% helix, 23% strand	P00491
U	Purine nucleoside phosphorylase (EC 2.4.2.1)	protein	285	35% helix, 23% strand	P00491

Ligands and binding sites

229 · 7-({[(1R,2S)-2,3-dihydroxy-1-(hydroxymethyl)propyl]amino}methyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 6 copies · chains E, Y, Q, S, U, T
SO4 · Sulfate ion · ion · 16 copies · chains E, Y, Q, S, T, U

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.81	0.98	20	empty
2	123	0.81	0.98	17	empty
3	124	0.80	0.98	32	SO4, 229
4	109	0.79	0.98	25	SO4, 229
5	105	0.79	0.98	25	SO4, 229

Interfaces

7 interfaces between chains.

Q–Y · 1338 Å² buried · 19 hydrogen bonds · protein-protein
E–Q · 1315 Å² buried · 15 hydrogen bonds · protein-protein
T–U · 1313 Å² buried · 20 hydrogen bonds · protein-protein
E–Y · 1310 Å² buried · 15 hydrogen bonds · protein-protein
S–T · 1310 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3K8O · Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-ImmH · the same entry in another collection · chain Y against Y, TM-score 1.00
P00491 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P00491) · a predicted model of the same protein · chain T 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 P00491
Elsewhere: RCSB PDB 3K8O · PDBe 3K8O · UniProt P00491

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