MolNFT v1 · #168258 · protein
Crystal structure of smcr N55I from vibrio vulnificus
6WAF · Luxr family transcriptional regulator: “Crystal structure of smcr N55I from vibrio vulnificus”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.73). MolNFT v1 #168258 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WAF
- Type
- protein
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luxr family transcriptional regulator
- UniProt
- Q9L8G8
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luxr family transcriptional regulator | protein | 201 | 63% helix, 1% strand | Q9L8G8 |
| B | Luxr family transcriptional regulator | protein | 197 | 66% helix, 1% strand | Q9L8G8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.73 | 0.81 | 51 | empty |
| 2 | 311 | 0.72 | 0.84 | 41 | empty |
| 3 | 163 | 0.54 | 0.80 | 25 | empty |
| 4 | 74 | 0.35 | 0.76 | 17 | empty |
| 5 | 62 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1561 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WAF · Crystal Structure of SmcR N55I 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 6WAF · PDBe 6WAF · UniProt Q9L8G8
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