Research workbench
1.65A resolution structure of bfrb (C89S, K96C) crystal form 1 from pseudomonas aeruginosa
Analyse 1.65A resolution structure of bfrb (C89S, K96C) crystal form 1 from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TOF
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- EC
- 1.16.3.1
- UniProt
- Q9HY79
- Ligands
- HEM, NA, K
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bacterioferritin (EC 1.16.3.1) | protein | 157 | 78% helix, 0% strand | Q9HY79 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · chains B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.71 | 0.87 | 30 | HEM |
| 2 | 342 | 0.59 | 0.76 | 32 | MPD |
| 3 | 218 | 0.46 | 0.74 | 22 | empty |
| 4 | 138 | 0.46 | 0.77 | 21 | MPD |
| 5 | 74 | 0.39 | 0.78 | 17 | MPD |
Interfaces
5 interfaces between chains.
- A–B · 904 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 516 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 514 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 505 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TOF · 1.65A resolution structure of BfrB (C89S, K96C) crystal form 1 from Pseudomonas aeruginosa · 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 4TOF · PDBe 4TOF · UniProt Q9HY79
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