MolNFT v1 · #50013 · protein
The crystal structure of a domain of protein VP0806 (unknown function) from vibrio parahaemolyticus rimd 2210633
2R5S · Uncharacterized protein VP0806: “The crystal structure of a domain of protein VP0806 (unknown function) from vibrio parahaemolyticus rimd…”. X-ray diffraction, 7 pockets (best druggability 0.45). MolNFT v1 #50013 on GenesisL1: 3D…
- PDB
- 2R5S
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein VP0806
- UniProt
- Q87RI8
- Pockets
- 7 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein VP0806 | protein | 171 | 74% helix, 0% strand | Q87RI8 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.45 | 0.78 | 18 | empty |
| 2 | 133 | 0.43 | 0.76 | 20 | empty |
| 3 | 125 | 0.41 | 0.75 | 17 | MES |
| 4 | 116 | 0.38 | 0.74 | 29 | empty |
| 5 | 76 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 816 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 2R5S · The crystal structure of a domain of protein VP0806 (unknown function) from Vibrio… · 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 Q87RI8
- Elsewhere: RCSB PDB 2R5S · PDBe 2R5S · UniProt Q87RI8
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