Research workbench
Crystal structure of VPA0735 from vibrio parahaemolyticus in monoclinic form, northeast structural genomics target VPR109
Analyse Crystal structure of VPA0735 from vibrio parahaemolyticus in monoclinic form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VB9
- Type
- protein
- Length
- 1,842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein VPA0735
- UniProt
- Q87I71
- Ligands
- MG
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Uncharacterized protein VPA0735 | protein | 460 | 28% helix, 26% strand | Q87I71 |
| B | Uncharacterized protein VPA0735 | protein | 462 | 28% helix, 26% strand | Q87I71 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.76 | 0.99 | 27 | MG |
| 2 | 67 | 0.75 | 0.99 | 25 | MG |
| 3 | 74 | 0.75 | 0.99 | 24 | empty |
| 4 | 65 | 0.75 | 0.99 | 23 | MG |
| 5 | 57 | 0.73 | 0.99 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3569 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3514 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 264 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 236 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 3VB9 · Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast… · 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 Q87I71
- Elsewhere: RCSB PDB 3VB9 · PDBe 3VB9 · UniProt Q87I71
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