Research workbench
1.60 a resolution structure of wt bfrb from pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 16)
Analyse 1.60 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
- 6NLN
- Type
- protein
- Length
- 1,872 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferroxidase
- EC
- 1.16.3.1
- UniProt
- Q9HY79
- Ligands
- KSY, HEM, FE2
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 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
- KSY · 4-{[3-(3-hydroxyphenyl)propyl]amino}-1H-isoindole-1, 3(2H)-dione · ligand · 13 copies · chains A, B, E, C, I, D, F, K, G, H, J, L
- HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains A, B, E, C, I, D, F, K, H, J, L
- FE2 · Fe (II) ion · metal · 3 copies · chains A, E, J, K, B, C, G, L, D, F, I
- PG4 · Tetraethylene glycol · additive · 27 copies · chains A, B, E, C, L, G, D, H, F, K, I, J
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 | 214 | 0.73 | 0.88 | 30 | HEM |
| 2 | 84 | 0.72 | 0.96 | 12 | empty |
| 3 | 217 | 0.72 | 0.87 | 33 | HEM |
| 4 | 212 | 0.72 | 0.87 | 32 | HEM |
| 5 | 231 | 0.71 | 0.86 | 31 | HEM |
Interfaces
27 interfaces between chains.
- F–K · 902 Ų buried · 12 hydrogen bonds · protein-protein
- C–I · 901 Ų buried · 12 hydrogen bonds · protein-protein
- H–J · 900 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 895 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 560 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6NLN · 1.60 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 6NLN · PDBe 6NLN · UniProt Q9HY79
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