MolNFT v1 · #124726 · protein
Crystal structure of mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with [3S,4R]-(4-(hypoxanthin-9- YL)PYRROLIDIN-3-yl)-oxymethanephosphonic acid
5KNP · Hypoxanthine-guanine phosphoribosyltransferase: “Crystal structure of mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex…”. X-ray diffraction, 3 ligands (6W7, POP, MG), 7 pockets (best druggability…
- PDB
- 5KNP
- Type
- protein
- Length
- 711 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
- P9WHQ9
- Ligands
- 6W7, POP, MG
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 177 | 26% helix, 34% strand | P9WHQ9 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 175 | 23% helix, 33% strand | P9WHQ9 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 178 | 23% helix, 31% strand | P9WHQ9 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 181 | 27% helix, 32% strand | P9WHQ9 |
Ligands and binding sites
- 6W7 · [(3~{S},4~{R})-4-(6-oxidanylidene-1~{H}-purin-9-yl) pyrrolidin-3-yl]oxymethylphosphonic acid · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.70 | 0.76 | 79 | 6W7, MG, POP |
| 2 | 380 | 0.61 | 0.77 | 41 | 6W7, MG, POP |
| 3 | 399 | 0.59 | 0.76 | 42 | 6W7, MG, POP |
| 4 | 114 | 0.49 | 0.81 | 31 | empty |
| 5 | 101 | 0.49 | 0.81 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1431 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1410 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 559 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 555 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KNP · Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WHQ9 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain B 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 5KNP · PDBe 5KNP · UniProt P9WHQ9
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