MolNFT v1 · #137389 · protein
Crystal structure of adenine phosphoribosyl transferase from trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5- phosphate
5VN4 · Adenine phosphoribosyltransferase, putative: “Crystal structure of adenine phosphoribosyl transferase from trypanosoma brucei in complex with AMP…”. X-ray diffraction, 4 ligands (ADE, HSX, PPV), 2 pockets (best druggability 0.75).…
- PDB
- 5VN4
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase, putative
- EC
- 2.4.2.7
- UniProt
- Q57V32
- Ligands
- ADE, HSX, PPV, MG
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase, putative (EC 2.4.2.7) | protein | 237 | 33% helix, 24% strand | Q57V32 |
| B | Adenine phosphoribosyltransferase, putative (EC 2.4.2.7) | protein | 231 | 34% helix, 24% strand | Q57V32 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.75 | 0.92 | 30 | ADE, HSX, PPV |
| 2 | 228 | 0.69 | 0.86 | 42 | ADE, HSX, PPV, MG |
Interfaces
1 interface between chains.
- A–B · 2748 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5VN4 · Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in… · 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 Q57V32
- Elsewhere: RCSB PDB 5VN4 · PDBe 5VN4 · UniProt Q57V32
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.