MolNFT v1 · #157388 · protein
Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex with xmp
6MXB · Hypoxanthine-guanine phosphoribosyltransferase, putative: “Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex…”. X-ray diffraction, 2 ligands (XMP, MG), 18 pockets (best…
- PDB
- 6MXB
- Type
- protein
- Length
- 1,280 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase, putative
- UniProt
- Q38CA1
- Ligands
- XMP, MG
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 216 | 24% helix, 31% strand | Q38CA1 |
| B | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 214 | 24% helix, 31% strand | Q38CA1 |
| C | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 215 | 24% helix, 33% strand | Q38CA1 |
| D | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 212 | 25% helix, 32% strand | Q38CA1 |
| E | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 210 | 25% helix, 31% strand | Q38CA1 |
| F | Hypoxanthine-guanine phosphoribosyltransferase, putative | protein | 213 | 25% helix, 32% strand | Q38CA1 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.77 | 0.79 | 127 | MG |
| 2 | 399 | 0.67 | 0.80 | 49 | empty |
| 3 | 84 | 0.66 | 0.92 | 20 | empty |
| 4 | 454 | 0.66 | 0.78 | 49 | XMP |
| 5 | 351 | 0.57 | 0.76 | 33 | XMP, MG |
Interfaces
5 interfaces between chains.
- A–B · 2264 Ų buried · 46 hydrogen bonds · protein-protein
- D–F · 2205 Ų buried · 37 hydrogen bonds · protein-protein
- C–E · 2133 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6MXB · Crystal structure of Trypanosoma brucei hypoxanthine-guanine-xanthine… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q38CA1
- Elsewhere: RCSB PDB 6MXB · PDBe 6MXB · UniProt Q38CA1
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