Research workbench
The crystal structure of type III effector protein xopq complexed with adenosine diphosphate ribose
Analyse The crystal structure of type III effector protein xopq complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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