Research workbench
Crystal structure of smcr N142D from vibrio vulnificus
Analyse Crystal structure of smcr N142D 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
- 6WAI
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luxr family transcriptional regulator
- UniProt
- Q9L8G8
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luxr family transcriptional regulator | protein | 200 | 68% helix, 2% strand | Q9L8G8 |
| B | Luxr family transcriptional regulator | protein | 202 | 70% helix, 0% strand | Q9L8G8 |
| C | Luxr family transcriptional regulator | protein | 203 | 68% helix, 1% strand | Q9L8G8 |
| D | Luxr family transcriptional regulator | protein | 199 | 71% helix, 1% strand | Q9L8G8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.77 | 0.86 | 49 | empty |
| 2 | 277 | 0.75 | 0.89 | 42 | empty |
| 3 | 426 | 0.72 | 0.82 | 44 | EDO |
| 4 | 267 | 0.69 | 0.84 | 39 | EDO |
| 5 | 200 | 0.61 | 0.82 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1592 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1530 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 179 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6WAI · Crystal Structure of SmcR N142D 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 Q9L8G8
- Elsewhere: RCSB PDB 6WAI · PDBe 6WAI · UniProt Q9L8G8
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