MolNFT v1 · #170744 · protein
Crystal structure of domains 4-5 of cnfy from yersinia pseudotuberculosis
6YHN · Cytotoxic necrotizing factor: “Crystal structure of domains 4-5 of cnfy from yersinia pseudotuberculosis”. X-ray diffraction, 4 ligands (MG, NA, CL), 6 pockets (best druggability 0.60). MolNFT v1 #170744 on GenesisL1: 3D structure…
- PDB
- 6YHN
- Type
- protein
- Length
- 460 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic necrotizing factor
- UniProt
- A0A0N9JNY6
- Ligands
- MG, NA, CL, SO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxic necrotizing factor | protein | 460 | 21% helix, 33% strand | A0A0N9JNY6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- BU3 · (R,R)-2,3-butanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.60 | 0.78 | 47 | MG |
| 2 | 197 | 0.51 | 0.77 | 26 | empty |
| 3 | 113 | 0.41 | 0.76 | 22 | CL |
| 4 | 83 | 0.39 | 0.78 | 19 | MG |
| 5 | 85 | 0.36 | 0.76 | 22 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6YHN · Crystal structure of domains 4-5 of CNFy from Yersinia pseudotuberculosis · 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 A0A0N9JNY6
- Elsewhere: RCSB PDB 6YHN · PDBe 6YHN · UniProt A0A0N9JNY6
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