MolNFT v1 · #152365 · protein
Crystal structure of vapbc from salmonella typhimurium
6IFC · TRNA(FMET)-specific endonuclease vapc: “Crystal structure of vapbc from salmonella typhimurium”. X-ray diffraction, 1 ligand (CA). MolNFT v1 #152365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IFC
- Type
- protein
- Length
- 628 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(FMET)-specific endonuclease vapc; Antitoxin vapb
- EC
- 3.1.-.-
- UniProt
- Q8ZM86, Q7CPV2
- Ligands
- CA
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 58% helix, 13% strand | Q8ZM86 |
| B, F | Antitoxin vapb | protein | 22 | 23% helix, 0% strand | Q7CPV2 |
| D, H | Antitoxin vapb | protein | 28 | 18% helix, 0% strand | Q7CPV2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
13 interfaces between chains.
- G–H · 1504 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1443 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1336 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 26 hydrogen bonds · protein-protein
- E–G · 1201 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6IFC · Crystal structure of VapBC from Salmonella typhimurium · the same entry in another collection · chain H against H, TM-score 1.00
- Q8ZM86 · AlphaFold monomer V2.0 prediction for TRNA(FMET)-specific endonuclease vapc (Q8ZM86) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q7CPV2 · AlphaFold monomer V2.0 prediction for antitoxin vapb (Q7CPV2) · a predicted model of the same protein · chain D against A, TM-score 0.60
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 Q8ZM86
- Every structure of UniProt Q7CPV2
- Elsewhere: RCSB PDB 6IFC · PDBe 6IFC · UniProt Q8ZM86 · UniProt Q7CPV2
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