Research workbench
Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase gmp complex
Analyse Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase gmp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QK3
- Type
- protein
- Length
- 899 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
- Q26997
- Ligands
- 5GP
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 228 | 29% helix, 24% strand | Q26997 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 231 | 29% helix, 23% strand | Q26997 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 213 | 31% helix, 25% strand | Q26997 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 227 | 30% helix, 26% strand | Q26997 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.88 | 0.89 | 132 | 5GP |
| 2 | 523 | 0.79 | 0.86 | 67 | empty |
| 3 | 427 | 0.77 | 0.86 | 65 | empty |
| 4 | 627 | 0.73 | 0.80 | 53 | 5GP |
| 5 | 83 | 0.53 | 0.85 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1705 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 907 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 808 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 432 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1QK3 · Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase gmp complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q26997 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine-xanthine… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q26997
- Elsewhere: RCSB PDB 1QK3 · PDBe 1QK3 · UniProt Q26997
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