Research workbench
Crystal structure of hypoxanthine-guanine-xanthine phosphorybosyltranferase in complex with {[(2S)-3-(2-amino-6-oxo-1,6- dihydro-9H-purin-9-YL)PROPANE-1,2-DIYL]BIS(OXYETHANE-2,1-diyl) }BIS(PHOSPHONIC acid)
Analyse Crystal structure of hypoxanthine-guanine-xanthine phosphorybosyltranferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQO
- Type
- protein
- Length
- 1,263 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- UniProt
- Q38CA1
- Ligands
- 45T, MG
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase | protein | 211 | 25% helix, 32% strand | Q38CA1 |
| B | Hypoxanthine-guanine phosphoribosyltransferase | protein | 212 | 25% helix, 31% strand | Q38CA1 |
| C, E | Hypoxanthine-guanine phosphoribosyltransferase | protein | 210 | 25% helix, 31% strand | Q38CA1 |
| D | Hypoxanthine-guanine phosphoribosyltransferase | protein | 209 | 25% helix, 31% strand | Q38CA1 |
| F | Hypoxanthine-guanine phosphoribosyltransferase | protein | 211 | 26% helix, 32% strand | Q38CA1 |
Ligands and binding sites
- 45T · {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) propane-1,2-diyl]bis(oxyethane-2,1-diyl) }bis(phosphonic acid) · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains D, 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 | 1109 | 0.77 | 0.79 | 107 | empty |
| 2 | 336 | 0.69 | 0.82 | 38 | empty |
| 3 | 314 | 0.56 | 0.76 | 32 | 45T |
| 4 | 279 | 0.53 | 0.75 | 34 | 45T |
| 5 | 259 | 0.52 | 0.75 | 34 | 45T |
Interfaces
5 interfaces between chains.
- B–F · 2145 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 2099 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2053 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 660 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 638 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation).
Compared structures
- 6AQO · 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 6AQO · PDBe 6AQO · UniProt Q38CA1
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