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Human hgprtase with transition state inhibitor

Analyse Human hgprtase with transition state inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BZY
Type: protein
Length: 856 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine-guanine phosphoribosyltransferase
EC: 2.4.2.8
UniProt: P00492
Ligands: IMU, POP, MG
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8)	protein	214	30% helix, 34% strand	P00492

Ligands and binding sites

IMU · Phosphoric acid mono-[5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-3,4-dihydroxy-pyrrolidin-2-ylmethyl] ester · ligand · 4 copies · chains A, B, C, D
POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1070	0.83	0.85	71	empty
2	223	0.79	0.93	32	MG, IMU, POP
3	202	0.79	0.93	33	MG, IMU, POP
4	321	0.76	0.88	48	MG, IMU, POP
5	314	0.76	0.88	49	MG, IMU, POP

Interfaces

6 interfaces between chains.

C–D · 1624 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1590 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 917 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 882 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 360 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1BZY · Human hgprtase with transition state inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P00492 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P00492
Elsewhere: RCSB PDB 1BZY · PDBe 1BZY · UniProt P00492

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