MolNFT v1 · #123172 · protein
Conformational changes during monomer-to-dimer transition of brucella suis VIRB8
5JBS · Type IV secretion system protein VIRB8: “Conformational changes during monomer-to-dimer transition of brucella suis VIRB8”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.76). MolNFT v1 #123172 on GenesisL1: 3D…
- PDB
- 5JBS
- Type
- protein
- Length
- 522 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV secretion system protein VIRB8
- UniProt
- Q7CEG3
- Ligands
- CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type IV secretion system protein VIRB8 | protein | 139 | 39% helix, 35% strand | Q7CEG3 |
| B | Type IV secretion system protein VIRB8 | protein | 126 | 37% helix, 39% strand | Q7CEG3 |
| C | Type IV secretion system protein VIRB8 | protein | 121 | 39% helix, 37% strand | Q7CEG3 |
| D | Type IV secretion system protein VIRB8 | protein | 136 | 39% helix, 36% strand | Q7CEG3 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.76 | 0.79 | 98 | PEG, EPE |
| 2 | 627 | 0.67 | 0.76 | 55 | empty |
| 3 | 167 | 0.52 | 0.78 | 21 | PEG, EPE |
| 4 | 81 | 0.38 | 0.77 | 13 | empty |
| 5 | 72 | 0.29 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 721 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 510 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 328 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 323 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5JBS · Conformational changes during monomer-to-dimer transition of Brucella suis VirB8 · the same entry in another collection · chain D against D, TM-score 1.00
- Q7CEG3 · AlphaFold monomer V2.0 prediction for type IV secretion system protein VIRB8 (Q7CEG3) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q7CEG3
- Elsewhere: RCSB PDB 5JBS · PDBe 5JBS · UniProt Q7CEG3
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