Research workbench
Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex with gmp
Analyse Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MXC
- Type
- protein
- Length
- 1,304 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- UniProt
- Q38CA1
- Ligands
- 5GP, MG
- Pockets
- 16 · 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 | protein | 218 | 24% helix, 32% strand | Q38CA1 |
| B | Hypoxanthine-guanine phosphoribosyltransferase | protein | 217 | 24% helix, 32% strand | Q38CA1 |
| C | Hypoxanthine-guanine phosphoribosyltransferase | protein | 220 | 24% helix, 32% strand | Q38CA1 |
| D | Hypoxanthine-guanine phosphoribosyltransferase | protein | 215 | 24% helix, 33% strand | Q38CA1 |
| E | Hypoxanthine-guanine phosphoribosyltransferase | protein | 216 | 24% helix, 32% strand | Q38CA1 |
| F | Hypoxanthine-guanine phosphoribosyltransferase | protein | 218 | 24% helix, 33% strand | Q38CA1 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.77 | 0.81 | 80 | empty |
| 2 | 395 | 0.68 | 0.81 | 51 | empty |
| 3 | 419 | 0.64 | 0.78 | 40 | 5GP, MG |
| 4 | 337 | 0.62 | 0.79 | 51 | empty |
| 5 | 344 | 0.60 | 0.77 | 34 | 5GP, MG |
Interfaces
5 interfaces between chains.
- A–B · 2307 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 2273 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2241 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 599 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6MXC · 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 6MXC · PDBe 6MXC · UniProt Q38CA1
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