Research workbench
Pseudomonas aeruginosa virulence factor regulator with camp ligand and CL(TRIETHYLPHOSPHINE)GOLD(I)
Analyse Pseudomonas aeruginosa virulence factor regulator with camp ligand and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FF9
- Type
- protein
- Length
- 1,552 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-activated global transcriptional regulator vfr
- UniProt
- P55222
- Ligands
- CMP, AU, CL, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Camp-activated global transcriptional regulator vfr | protein | 197 | 37% helix, 27% strand | P55222 |
| B | Camp-activated global transcriptional regulator vfr | protein | 195 | 34% helix, 28% strand | P55222 |
| D | Camp-activated global transcriptional regulator vfr | protein | 198 | 36% helix, 28% strand | P55222 |
| E | Camp-activated global transcriptional regulator vfr | protein | 194 | 39% helix, 30% strand | P55222 |
| F | Camp-activated global transcriptional regulator vfr | protein | 188 | 34% helix, 29% strand | P55222 |
| H | Camp-activated global transcriptional regulator vfr | protein | 186 | 35% helix, 31% strand | P55222 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- AU · Gold ion · metal · 31 copies · chains A, B, C, G, D, E, F, H
- CL · Chloride ion · ion · 14 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 3 copies · chains C, G, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.80 | 0.87 | 59 | CMP |
| 2 | 685 | 0.80 | 0.84 | 80 | CMP |
| 3 | 1065 | 0.78 | 0.80 | 92 | AU, CL |
| 4 | 537 | 0.78 | 0.85 | 67 | CMP, AU |
| 5 | 301 | 0.75 | 0.87 | 50 | CMP, AU |
Interfaces
13 interfaces between chains.
- A–B · 1753 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1740 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1721 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1650 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 525 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7FF9 · Pseudomonas aeruginosa Virulence Factor Regulator with cAMP ligand and… · the same entry in another collection · chain H against H, TM-score 1.00
- P55222 · AlphaFold monomer V2.0 prediction for camp-activated global transcriptional regulator vfr… · a predicted model of the same protein · chain E 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 P55222
- Elsewhere: RCSB PDB 7FF9 · PDBe 7FF9 · UniProt P55222
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