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Crystal structure of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with XMP
Analyse Crystal structure of Trypanosoma brucei hypoxanthine-guanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MXG
- Type
- protein
- Length
- 343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.392
- Source
- Trypanosoma brucei brucei
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q07010
- Ligands
- XMP, MG, SO4
- Pockets
- 7 · best druggability 0.38
Structure
x-ray diffraction · resolution 2.392 · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 171 | 26% helix, 26% strand | Q07010 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 172 | 30% helix, 30% strand | Q07010 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.38 | 0.75 | 20 | XMP, SO4 |
| 2 | 67 | 0.38 | 0.79 | 15 | empty |
| 3 | 97 | 0.38 | 0.75 | 22 | XMP, MG, SO4 |
| 4 | 75 | 0.35 | 0.76 | 14 | empty |
| 5 | 61 | 0.34 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1508 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6MXG · 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 6MXG · PDBe 6MXG · UniProt Q07010
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