Crystal structure of mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with (3-((3R,4R)-3-(guanin-9- yl)-4-((S)-2-hydroxy-2-PHOSPHONOETHOXY)PYRROLIDIN-1-yl)-3-oxopropyl) phosphonic acid

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 33% strand (DSSP).

Ligands and binding sites

• YPG · [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 1443 Ų buried · 16 hydrogen bonds · protein-protein
• A–B · 1426 Ų buried · 17 hydrogen bonds · protein-protein
• A–D · 765 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 753 Ų buried · 13 hydrogen bonds · protein-protein
• A–C · 94 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5KNY · Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine… · the same entry in another collection · chain A against A, TM-score 1.00
• P9WHQ9 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P9WHQ9
• Elsewhere: RCSB PDB 5KNY · PDBe 5KNY · UniProt P9WHQ9