MolNFT v1 · #143117 · protein
Crystal structure of trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with (2-{[2-(2-amino-6-oxo-1,6- dihydro-9H-purin-9-YL)ETHYL](3-AMINOPROPYL)AMINO}ETHYL)PHOSPHONIC acid
6APU · Hypoxanthine-guanine phosphoribosyltransferase: “Crystal structure of trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with…”. X-ray diffraction, 3 ligands (3L6, MG, SO4), 5 pockets (best druggability…
- PDB
- 6APU
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q07010
- Ligands
- 3L6, MG, SO4
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 177 | 34% helix, 31% strand | Q07010 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 177 | 34% helix, 30% strand | Q07010 |
Ligands and binding sites
- 3L6 · (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) ethyl](3-aminopropyl)amino}ethyl)phosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.46 | 0.74 | 26 | SO4, MG, 3L6 |
| 2 | 97 | 0.39 | 0.76 | 18 | empty |
| 3 | 90 | 0.37 | 0.77 | 16 | PEG |
| 4 | 110 | 0.36 | 0.74 | 22 | SO4, MG, 3L6 |
| 5 | 67 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1602 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6APU · Crystal structure of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in… · the same entry in another collection · chain A against A, 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 0.99
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 6APU · PDBe 6APU · UniProt Q07010
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