MolNFT v1 · #90017 · protein
2.0 a resolution structure of pseudomonas aeruginosa bacterioferritin (bfrb) in complex with bacterioferritin associated ferredoxin (bfd)
4E6K: “2.0 a resolution structure of pseudomonas aeruginosa bacterioferritin (bfrb) in complex with bacterioferritin…”. X-ray diffraction, 5 ligands (HEM, FES, NA), 14 pockets (best druggability 0.72). MolNFT v1 #90017 on GenesisL1: 3D…
- PDB
- 4E6K
- Type
- protein
- Length
- 1,086 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin; Bacterioferritin-associated ferredoxin
- UniProt
- Q9HY79, Q9HY80
- Ligands
- HEM, FES, NA, K, PO4
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Bacterioferritin | protein | 157 | 78% helix, 0% strand | Q9HY79 |
| D, E | Bacterioferritin | protein | 156 | 78% helix, 0% strand | Q9HY79 |
| G | Bacterioferritin-associated ferredoxin | protein | 57 | 54% helix, 9% strand | Q9HY80 |
| H | Bacterioferritin-associated ferredoxin | protein | 33 | 36% helix, 15% strand | Q9HY80 |
| I | Bacterioferritin-associated ferredoxin | protein | 56 | 55% helix, 9% strand | Q9HY80 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C, D, E, F
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains B, G, C, H, E, I
- NA · Sodium ion · metal · 6 copies · chains A, B, C, E, D, F
- K · Potassium ion · metal · 3 copies · chains A, B, C, E, F
- PO4 · Phosphate ion · ion · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.72 | 0.87 | 33 | HEM |
| 2 | 215 | 0.72 | 0.87 | 31 | HEM |
| 3 | 205 | 0.71 | 0.87 | 31 | HEM |
| 4 | 326 | 0.59 | 0.77 | 34 | empty |
| 5 | 296 | 0.56 | 0.76 | 30 | empty |
Interfaces
14 interfaces between chains.
- A–B · 925 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 910 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 529 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 517 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4E6K · 2.0 A resolution structure of Pseudomonas aeruginosa bacterioferritin (BfrB) in complex… · 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
- Every structure of UniProt Q9HY80
- Elsewhere: RCSB PDB 4E6K · PDBe 4E6K · UniProt Q9HY79 · UniProt Q9HY80
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