Research workbench
Crystal structure of the yaeq family protein VPA0551 from vibrio parahaemolyticus
Analyse Crystal structure of the yaeq family protein VPA0551 from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TCB
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yaeq family protein VPA0551
- UniProt
- Q87IQ5
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yaeq family protein VPA0551 | protein | 171 | 26% helix, 43% strand | Q87IQ5 |
| B | Yaeq family protein VPA0551 | protein | 176 | 27% helix, 42% strand | Q87IQ5 |
| C | Yaeq family protein VPA0551 | protein | 173 | 26% helix, 43% strand | Q87IQ5 |
| D | Yaeq family protein VPA0551 | protein | 172 | 27% helix, 42% strand | Q87IQ5 |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.74 | 0.77 | 90 | empty |
| 2 | 322 | 0.55 | 0.76 | 52 | empty |
| 3 | 96 | 0.43 | 0.79 | 23 | empty |
| 4 | 71 | 0.36 | 0.78 | 17 | empty |
| 5 | 95 | 0.36 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 624 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 510 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 144 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 7TCB · Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus · 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 Q87IQ5
- Elsewhere: RCSB PDB 7TCB · PDBe 7TCB · UniProt Q87IQ5
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