Research workbench
Crystal structure of the VPA0106 protein from vibrio parahaemolyticus. northeast structural genomics consortium target VPR106.
Analyse Crystal structure of the VPA0106 protein from vibrio parahaemolyticus.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U07
- Type
- protein
- Length
- 1,195 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein VPA0106
- UniProt
- Q87JZ2
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein VPA0106 | protein | 398 | 30% helix, 27% strand | Q87JZ2 |
| C | Uncharacterized protein VPA0106 | protein | 399 | 30% helix, 27% strand | Q87JZ2 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.68 | 0.78 | 43 | empty |
| 2 | 570 | 0.68 | 0.78 | 61 | empty |
| 3 | 496 | 0.68 | 0.79 | 47 | empty |
| 4 | 332 | 0.57 | 0.76 | 37 | empty |
| 5 | 310 | 0.55 | 0.75 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 430 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 418 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 modified, 3 disulfide (engineered, disulfide).
Compared structures
- 3U07 · Crystal Structure of the VPA0106 protein from Vibrio parahaemolyticus. 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 Q87JZ2
- Elsewhere: RCSB PDB 3U07 · PDBe 3U07 · UniProt Q87JZ2
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