Research workbench
Trypanosome brucei hypoxanthine-guanine phosphoribosyltranferase in complex with a 9-[5-(PHOSPHONOHEPTYL]HYPOXANTHINE
Analyse Trypanosome brucei hypoxanthine-guanine phosphoribosyltranferase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K51
- Type
- protein
- Length
- 664 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
- Q07010
- Ligands
- 6QD
- Pockets
- 14 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 167 | 31% helix, 29% strand | Q07010 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 167 | 35% helix, 30% strand | Q07010 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 161 | 30% helix, 30% strand | Q07010 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 169 | 31% helix, 30% strand | Q07010 |
Ligands and binding sites
- 6QD · 5-(6-oxidanylidene-3~{H}-purin-9-yl)pentylphosphonic 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.45 | 0.76 | 19 | empty |
| 2 | 72 | 0.39 | 0.79 | 14 | empty |
| 3 | 92 | 0.39 | 0.76 | 16 | empty |
| 4 | 97 | 0.37 | 0.75 | 20 | 6QD |
| 5 | 82 | 0.36 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1475 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1428 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 482 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5K51 · Trypanosome brucei Hypoxanthine-guanine phosphoribosyltranferase in complex with a… · the same entry in another collection · chain D against D, TM-score 1.00
- Q07010 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q07010
- Elsewhere: RCSB PDB 5K51 · PDBe 5K51 · UniProt Q07010
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.