MolNFT v1 · #105866 · protein
Crystal structures of mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease
4RHT · Hypoxanthine-guanine phosphoribosyltransferase hpt: “Crystal structures of mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential…”. X-ray diffraction, 3 ligands (POP, 5GP, MG), 8 pockets (best…
- PDB
- 4RHT
- Type
- protein
- Length
- 655 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase hpt
- UniProt
- I6YCM5
- Ligands
- POP, 5GP, MG
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase hpt | protein | 166 | 27% helix, 36% strand | I6YCM5 |
| B | Hypoxanthine-guanine phosphoribosyltransferase hpt | protein | 166 | 26% helix, 36% strand | I6YCM5 |
| C | Hypoxanthine-guanine phosphoribosyltransferase hpt | protein | 161 | 22% helix, 32% strand | I6YCM5 |
| D | Hypoxanthine-guanine phosphoribosyltransferase hpt | protein | 162 | 22% helix, 32% strand | I6YCM5 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- 5GP · Guanosine-5'-monophosphate · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.56 | 0.76 | 38 | POP, 5GP, MG |
| 2 | 381 | 0.56 | 0.74 | 49 | POP, 5GP, MG |
| 3 | 317 | 0.55 | 0.75 | 43 | POP, 5GP, MG |
| 4 | 262 | 0.53 | 0.75 | 32 | POP, 5GP, MG |
| 5 | 130 | 0.51 | 0.80 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1317 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1246 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 596 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RHT · Crystal structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
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 I6YCM5
- Elsewhere: RCSB PDB 4RHT · PDBe 4RHT · UniProt I6YCM5
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