MolNFT v1 · #143157 · protein
Crystal structure of hypoxanthine-guanine-xanthine phosphorybosyltranferase in complex with [(2-{[2-(2-amino-6-oxo-1,6- dihydro-9H-purin-9-YL)ETHYL][(E)-2-PHOSPHONOETHENYL]AMINO}ETHOXY) METHYL]PHOSPHONIC acid
6AR9 · Hypoxanthine-guanine phosphoribosyltransferase, putative: “Crystal structure of hypoxanthine-guanine-xanthine phosphorybosyltranferase in complex with…”. X-ray diffraction, 2 ligands (3L4, MG), 16 pockets (best druggability 0.77).…
- PDB
- 6AR9
- Type
- protein
- Length
- 1,271 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase, putative
- UniProt
- Q38CA1
- Ligands
- 3L4, MG
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 214 | 24% helix, 31% strand | Q38CA1 |
| B | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 212 | 25% helix, 32% strand | Q38CA1 |
| C, D | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 209 | 25% helix, 32% strand | Q38CA1 |
| E | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 214 | 24% helix, 33% strand | Q38CA1 |
| F | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 213 | 24% helix, 32% strand | Q38CA1 |
Ligands and binding sites
- 3L4 · [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) ethyl][(e)-2-phosphonoethenyl]amino}ethoxy) methyl]phosphonic acid · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 7 copies · chains A, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.77 | 0.81 | 78 | empty |
| 2 | 385 | 0.67 | 0.80 | 50 | empty |
| 3 | 360 | 0.58 | 0.76 | 35 | 3L4, MG |
| 4 | 326 | 0.56 | 0.76 | 54 | empty |
| 5 | 315 | 0.56 | 0.76 | 33 | 3L4, MG |
Interfaces
5 interfaces between chains.
- E–F · 2292 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2193 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2173 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 624 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 581 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (oxidation).
Compared structures
- 6AR9 · Crystal structure of hypoxanthine-guanine-xanthine phosphorybosyltranferase in complex… · 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 Q38CA1
- Elsewhere: RCSB PDB 6AR9 · PDBe 6AR9 · UniProt Q38CA1
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