MolNFT v1 · #138035 · protein
Crystal structure of rrsp, a martx toxin effector domain from vibrio vulnificus CMCP6
5W6L · Rtx repeat-containing cytotoxin: “Crystal structure of rrsp, a martx toxin effector domain from vibrio vulnificus CMCP6”. X-ray diffraction, 2 ligands (SO4, CL), 13 pockets (best druggability 0.58). MolNFT v1 #138035 on GenesisL1…
- PDB
- 5W6L
- Type
- protein
- Length
- 986 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rtx repeat-containing cytotoxin
- UniProt
- A0A1V8MQR3
- Ligands
- SO4, CL
- Pockets
- 13 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rtx repeat-containing cytotoxin | protein | 494 | 55% helix, 9% strand | A0A1V8MQR3 |
| B | Rtx repeat-containing cytotoxin | protein | 492 | 56% helix, 8% strand | A0A1V8MQR3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.58 | 0.75 | 40 | empty |
| 2 | 255 | 0.58 | 0.78 | 40 | empty |
| 3 | 232 | 0.56 | 0.78 | 47 | empty |
| 4 | 150 | 0.45 | 0.76 | 22 | empty |
| 5 | 114 | 0.40 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5W6L · Crystal Structure of RRSP, a MARTX Toxin Effector Domain from Vibrio vulnificus CMCP6 · 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 A0A1V8MQR3
- Elsewhere: RCSB PDB 5W6L · PDBe 5W6L · UniProt A0A1V8MQR3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.