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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: 4RHU
Type: protein
Length: 1,042 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine-guanine phosphoribosyltransferase hpt
UniProt: I6YCM5
Ligands: 45T, 3QE, MG
Pockets: 16 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 25% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypoxanthine-guanine phosphoribosyltransferase hpt	protein	180	26% helix, 33% strand	I6YCM5
B	Hypoxanthine-guanine phosphoribosyltransferase hpt	protein	178	22% helix, 34% strand	I6YCM5
C	Hypoxanthine-guanine phosphoribosyltransferase hpt	protein	175	25% helix, 33% strand	I6YCM5
D	Hypoxanthine-guanine phosphoribosyltransferase hpt	protein	168	26% helix, 33% strand	I6YCM5
E	Hypoxanthine-guanine phosphoribosyltransferase hpt	protein	169	27% helix, 30% strand	I6YCM5
F	Hypoxanthine-guanine phosphoribosyltransferase hpt	protein	172	24% helix, 34% strand	I6YCM5

Ligands and binding sites

45T · {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) propane-1,2-diyl]bis(oxyethane-2,1-diyl) }bis(phosphonic acid) · ligand · 4 copies · chains C, D, E, F
3QE · {[(2R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid) · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	749	0.72	0.78	52	45T, MG
2	171	0.61	0.83	34	empty
3	419	0.60	0.75	42	3QE, MG
4	320	0.58	0.76	40	3QE, MG
5	183	0.55	0.80	24	empty

Interfaces

9 interfaces between chains.

A–B · 1433 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1416 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1372 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 659 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 501 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4RHU · 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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Every structure of UniProt I6YCM5
Elsewhere: RCSB PDB 4RHU · PDBe 4RHU · UniProt I6YCM5

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