Research workbench
Crystal structure of the domain of putative sensory BOX/GGDEF family protein from vibrio parahaemolyticus
Analyse Crystal structure of the domain of putative sensory BOX/GGDEF family protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P7J
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sensory BOX/GGDEF family protein
- UniProt
- Q87SR8
- Ligands
- NA, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sensory BOX/GGDEF family protein | protein | 265 | 35% helix, 34% strand | Q87SR8 |
| B | Putative sensory BOX/GGDEF family protein | protein | 274 | 36% helix, 34% strand | Q87SR8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACY · Acetic acid · additive · chains 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 | 718 | 0.80 | 0.84 | 83 | SO4, ACY |
| 2 | 115 | 0.55 | 0.83 | 21 | empty |
| 3 | 96 | 0.53 | 0.84 | 21 | empty |
| 4 | 85 | 0.34 | 0.75 | 22 | empty |
| 5 | 59 | 0.34 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2P7J · Crystal structure of the domain of putative sensory box/GGDEF family protein 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 Q87SR8
- Elsewhere: RCSB PDB 2P7J · PDBe 2P7J · UniProt Q87SR8
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