Research workbench
1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-50
Analyse 1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5F
- Type
- protein
- Length
- 1,872 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Pseudomonas aeruginosa
- Molecule
- Ferroxidase
- EC
- 1.16.3.1
- UniProt
- Q9HY79
- Ligands
- HEM, VXP, K
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.95 · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Ferroxidase (EC 1.16.3.1) | protein | 156 | 78% helix, 0% strand | Q9HY79 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains A, B, E, C, I, D, F, K, H, J, L
- VXP · 4-{[(3-chloro-5-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione · ligand · 6 copies · chains D, B, E, H, J, F, K, L
- K · Potassium ion · metal · 3 copies · chains A, E, J, K, B, C, G, L, D, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.73 | 0.89 | 31 | HEM |
| 2 | 84 | 0.73 | 0.96 | 12 | empty |
| 3 | 203 | 0.72 | 0.88 | 33 | HEM |
| 4 | 210 | 0.71 | 0.87 | 33 | HEM |
| 5 | 74 | 0.71 | 0.96 | 12 | empty |
Interfaces
27 interfaces between chains.
- B–E · 907 Ų buried · 12 hydrogen bonds · protein-protein
- C–I · 906 Ų buried · 12 hydrogen bonds · protein-protein
- H–J · 900 Ų buried · 12 hydrogen bonds · protein-protein
- F–K · 900 Ų buried · 12 hydrogen bonds · protein-protein
- D–K · 564 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7K5F · 1.90 a resolution structure of wt bfrb from pseudomonas aeruginosa in complex with a… · the same entry in another collection · chain A against A, 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 Q9HY79
- Elsewhere: RCSB PDB 7K5F · PDBe 7K5F · UniProt Q9HY79
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.