MolNFT v1 · #153008 · protein
Cryo-EM structure of an extracellular contractile injection system, pvc SHEATH/TUBE terminator in extended state
6J0F · PVC16: “Cryo-EM structure of an extracellular contractile injection system, pvc SHEATH/TUBE terminator in extended…”. Electron microscopy, 20 pockets (best druggability 0.74). MolNFT v1 #153008 on GenesisL1: 3D structure, binding…
- PDB
- 6J0F
- Type
- protein
- Length
- 2,472 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PVC16; PVC1
- UniProt
- B6VNM9, B6VNP4
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 2 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | PVC16 | protein | 272 | 25% helix, 24% strand | B6VNM9 |
| a, b, c, d, e, f | PVC1 | protein | 140 | 4% helix, 49% strand | B6VNP4 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.74 | 0.85 | 42 | empty |
| 2 | 366 | 0.74 | 0.85 | 42 | empty |
| 3 | 414 | 0.73 | 0.84 | 52 | empty |
| 4 | 371 | 0.73 | 0.85 | 42 | empty |
| 5 | 346 | 0.73 | 0.85 | 45 | empty |
Interfaces
36 interfaces between chains.
- A–B · 1762 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 1756 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1755 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1755 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1755 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6J0F · Cryo-EM Structure of an Extracellular Contractile Injection System, PVC sheath/tube… · the same entry in another collection · chain D against D, 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 B6VNM9
- Every structure of UniProt B6VNP4
- Elsewhere: RCSB PDB 6J0F · PDBe 6J0F · UniProt B6VNM9 · UniProt B6VNP4
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