MolNFT v1 · #103078 · protein
The crystal structure of type III effector protein xopq complexed with adenosine diphosphate ribose
4P5F · Inosine-uridine nucleoside N-ribohydrolase: “The crystal structure of type III effector protein xopq complexed with adenosine diphosphate ribose”. X-ray diffraction, 2 ligands (AR6, CA), 6 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4P5F
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-uridine nucleoside N-ribohydrolase
- UniProt
- Q5GUA3
- Ligands
- AR6, CA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-uridine nucleoside N-ribohydrolase | protein | 355 | 52% helix, 14% strand | Q5GUA3 |
| B | Inosine-uridine nucleoside N-ribohydrolase | protein | 345 | 52% helix, 15% strand | Q5GUA3 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains B
- CA · Calcium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.81 | 0.92 | 47 | AR6 |
| 2 | 837 | 0.76 | 0.80 | 86 | empty |
| 3 | 362 | 0.59 | 0.76 | 41 | empty |
| 4 | 100 | 0.49 | 0.81 | 19 | empty |
| 5 | 113 | 0.44 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 502 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4P5F · The crystal structure of type III effector protein XopQ complexed with adenosine… · 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 Q5GUA3
- Elsewhere: RCSB PDB 4P5F · PDBe 4P5F · UniProt Q5GUA3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.