MolNFT v1 · #92178 · protein
High resolution structure of truncated bacteriocin syringacin M from pseudomonas syringae pv. tomato DC3000
4FZL: “High resolution structure of truncated bacteriocin syringacin M from pseudomonas syringae pv. tomato DC3000”. X-ray diffraction, 3 ligands (CA, MG, CL), 3 pockets (best druggability 0.57). MolNFT v1 #92178 on GenesisL1: 3D…
- PDB
- 4FZL
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriocin
- UniProt
- Q88A25
- Ligands
- CA, MG, CL
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriocin | protein | 239 | 45% helix, 21% strand | Q88A25 |
| B | Bacteriocin | protein | 242 | 46% helix, 21% strand | Q88A25 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.57 | 0.75 | 33 | empty |
| 2 | 99 | 0.34 | 0.74 | 22 | EDO |
| 3 | 53 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4FZL · High resolution structure of truncated bacteriocin syringacin M from Pseudomonas syringae… · 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 Q88A25
- Elsewhere: RCSB PDB 4FZL · PDBe 4FZL · UniProt Q88A25
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