Research workbench
Crystal structure of vvplpa G389N from vibrio vulnificus
Analyse Crystal structure of vvplpa G389N from vibrio vulnificus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JL2
- Type
- protein
- Length
- 1,178 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermolabile hemolysin
- UniProt
- A0A2S3SYP4
- Ligands
- 1PS
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermolabile hemolysin | protein | 401 | 39% helix, 18% strand | A0A2S3SYP4 |
| B | Thermolabile hemolysin | protein | 391 | 38% helix, 19% strand | A0A2S3SYP4 |
| C | Thermolabile hemolysin | protein | 386 | 38% helix, 19% strand | A0A2S3SYP4 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 7 copies · chains A, B, C
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.81 | 0.96 | 33 | P6G |
| 2 | 591 | 0.79 | 0.85 | 61 | 1PS |
| 3 | 586 | 0.78 | 0.84 | 69 | 1PS |
| 4 | 603 | 0.78 | 0.84 | 63 | 1PS |
| 5 | 214 | 0.77 | 0.91 | 44 | P6G |
Interfaces
3 interfaces between chains.
- B–C · 786 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 649 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6JL2 · Crystal structure of VvPlpA G389N from Vibrio vulnificus · 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 A0A2S3SYP4
- Elsewhere: RCSB PDB 6JL2 · PDBe 6JL2 · UniProt A0A2S3SYP4
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