MolNFT v1 · #152375 · protein + DNA
Crystal structure of DNA bound vapbc from salmonella typhimurium
6IFM · TRNA(FMET)-specific endonuclease vapc: “Crystal structure of DNA bound vapbc from salmonella typhimurium”. X-ray diffraction, 9 pockets (best druggability 0.71). MolNFT v1 #152375 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6IFM
- Type
- protein + DNA
- Length
- 854 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(FMET)-specific endonuclease vapc; Antitoxin vapb; DNA forward (27-mer); DNA backward…
- EC
- 3.1.-.-
- UniProt
- Q8ZM86, Q7CPV2
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, C, G | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 56% helix, 9% strand | Q8ZM86 |
| B, F, H, D | Antitoxin vapb | protein | 68 | 7% helix, 35% strand | Q7CPV2 |
| M | DNA forward (27-mer) | dna | 27 | — | — |
| N | DNA backward (27-mer) | dna | 27 | — | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.71 | 0.76 | 96 | empty |
| 2 | 605 | 0.64 | 0.75 | 60 | empty |
| 3 | 177 | 0.48 | 0.76 | 31 | empty |
| 4 | 100 | 0.41 | 0.77 | 19 | empty |
| 5 | 58 | 0.39 | 0.80 | 15 | empty |
Interfaces
28 interfaces between chains.
- B–H · 1887 Ų buried · 39 hydrogen bonds · protein-protein
- F–D · 1839 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1574 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1558 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1415 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6IFM · Crystal structure of DNA bound VapBC from Salmonella typhimurium · the same entry in another collection · chain N against N, 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 B against A, TM-score 0.61
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 6IFM · PDBe 6IFM · UniProt Q8ZM86 · UniProt Q7CPV2
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