Research workbench
Crystal structure of human hypoxanthine guanine phosphoribzosyltransferase in complex with (4S,7S)-7-hydroxy-4- ((guanin-9-YL)METHYL)-2,5-dioxaheptan-1,7-diphosphonate
Analyse Crystal structure of human hypoxanthine guanine phosphoribzosyltransferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SAN
- Type
- protein
- Length
- 788 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
- P00492
- Ligands
- 8QI
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 196 | 30% helix, 30% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 195 | 30% helix, 29% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 199 | 30% helix, 28% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 198 | 32% helix, 27% strand | P00492 |
Ligands and binding sites
- 8QI · ({(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2S)-2-hydroxy-2-phosphonoethoxy]propoxy}methyl) phosphonic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.78 | 0.80 | 107 | empty |
| 2 | 315 | 0.64 | 0.80 | 33 | empty |
| 3 | 271 | 0.60 | 0.79 | 30 | empty |
| 4 | 142 | 0.42 | 0.75 | 20 | 8QI |
| 5 | 72 | 0.42 | 0.80 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1560 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1545 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 870 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7SAN · Crystal structure of human hypoxanthine guanine phosphoribzosyltransferase 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 P00492
- Elsewhere: RCSB PDB 7SAN · PDBe 7SAN · UniProt P00492
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