Research workbench
Crystal structure of trypanosome brucei hypoxanthine-guanine-xanthine phosphoribzosyltransferase in complex with (4S,7S)-7-hydroxy-4- ((guanin-9-YL)METHYL)-2,5-dioxaheptan-1,7-diphosphonate
Analyse Crystal structure of trypanosome brucei hypoxanthine-guanine-xanthine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SCR
- Type
- protein
- Length
- 1,274 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q38CA1
- Ligands
- 8QI
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 215 | 25% helix, 30% strand | Q38CA1 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 210 | 25% helix, 31% strand | Q38CA1 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 215 | 24% helix, 31% strand | Q38CA1 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 212 | 24% helix, 31% strand | Q38CA1 |
| E | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 211 | 24% helix, 31% strand | Q38CA1 |
| F | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 211 | 26% helix, 31% strand | Q38CA1 |
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 · 6 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.77 | 0.81 | 84 | empty |
| 2 | 341 | 0.69 | 0.82 | 53 | empty |
| 3 | 384 | 0.63 | 0.78 | 34 | 8QI |
| 4 | 343 | 0.58 | 0.76 | 37 | 8QI |
| 5 | 50 | 0.57 | 0.91 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–F · 2203 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 2184 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2116 Ų buried · 41 hydrogen bonds · protein-protein
- B–E · 652 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7SCR · Crystal structure of trypanosome brucei hypoxanthine-guanine-xanthine… · 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 7SCR · PDBe 7SCR · UniProt Q38CA1
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