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Crystal structures of mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease

Analyse Crystal structures of mycobacterium tuberculosis 6-oxopurine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RHY
Type: protein
Length: 700 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine-guanine phosphoribosyltransferase
UniProt: A5U8U8
Ligands: 3QG, MG
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 25% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypoxanthine-guanine phosphoribosyltransferase	protein	172	26% helix, 35% strand	A5U8U8
B	Hypoxanthine-guanine phosphoribosyltransferase	protein	173	25% helix, 35% strand	A5U8U8
C	Hypoxanthine-guanine phosphoribosyltransferase	protein	177	25% helix, 34% strand	A5U8U8
D	Hypoxanthine-guanine phosphoribosyltransferase	protein	178	24% helix, 34% strand	A5U8U8

Ligands and binding sites

3QG · [2-({2-[bis(2-phosphonoethyl)amino]ethyl}[2-(6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl]amino)ethyl]phosphonic acid · 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

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.63	0.88	27	empty
2	394	0.60	0.76	40	MG, 3QG
3	155	0.59	0.83	30	empty
4	369	0.59	0.76	40	MG, 3QG
5	356	0.58	0.76	35	MG, 3QG

Interfaces

6 interfaces between chains.

C–D · 1440 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1429 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 649 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 602 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 94 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4RHY · Crystal structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A5U8U8
Elsewhere: RCSB PDB 4RHY · PDBe 4RHY · UniProt A5U8U8

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