MolNFT v1 · #143118 · protein
Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) ETHYL][(E)-2-PHOSPHONOETHENYL]AMINO}ETHOXY)METHYL]PHOSPHONIC acid
6APV · Hypoxanthine-guanine phosphoribosyltransferase: “Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with…”. X-ray diffraction, 2 ligands (3L4, MG), 8 pockets (best druggability 0.48). MolNFT v1 #143118 on…
- PDB
- 6APV
- Type
- protein
- Length
- 708 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
- 3L4, MG
- Pockets
- 8 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 175 | 34% helix, 31% strand | Q07010 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 183 | 37% helix, 30% strand | Q07010 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 174 | 34% helix, 32% strand | Q07010 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 176 | 33% helix, 31% strand | Q07010 |
Ligands and binding sites
- 3L4 · [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) ethyl][(e)-2-phosphonoethenyl]amino}ethoxy) methyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.48 | 0.77 | 34 | empty |
| 2 | 166 | 0.45 | 0.75 | 22 | 3L4, MG |
| 3 | 164 | 0.45 | 0.75 | 27 | 3L4, MG |
| 4 | 163 | 0.43 | 0.74 | 24 | 3L4, MG |
| 5 | 123 | 0.42 | 0.76 | 24 | 3L4, MG |
Interfaces
3 interfaces between chains.
- A–B · 1634 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 388 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 204 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6APV · Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with… · 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 C 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 6APV · PDBe 6APV · UniProt Q07010
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