Research workbench
2.05A resolution structure of bfrb (D34F) from pseudomonas aeruginosa
Analyse 2.05A resolution structure of bfrb (D34F) from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TOD
- Type
- protein
- Length
- 3,699 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- EC
- 1.16.3.1
- UniProt
- Q9HY79
- Ligands
- HEM, K
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacterioferritin (EC 1.16.3.1) | protein | 153 | 80% helix, 0% strand | Q9HY79 |
| B, D, E, F, G, I, J, K, L, M, N, O, P, Q, S, T, U, V, X | Bacterioferritin (EC 1.16.3.1) | protein | 154 | 79% helix, 0% strand | Q9HY79 |
| C, H, R, W | Bacterioferritin (EC 1.16.3.1) | protein | 155 | 80% helix, 0% strand | Q9HY79 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- K · Potassium ion · metal · 6 copies · chains A, L, M, X, B, D, F, H, C, K, S, U, E, J, Q, V, G, I, O, W, N, P, R, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.74 | 0.88 | 32 | HEM |
| 2 | 88 | 0.73 | 0.95 | 14 | empty |
| 3 | 222 | 0.73 | 0.88 | 32 | HEM |
| 4 | 215 | 0.73 | 0.88 | 34 | HEM |
| 5 | 209 | 0.72 | 0.88 | 30 | HEM |
Interfaces
72 interfaces between chains.
- G–H · 958 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 946 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 946 Ų buried · 12 hydrogen bonds · protein-protein
- S–T · 945 Ų buried · 12 hydrogen bonds · protein-protein
- Q–R · 942 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4TOD · 2.05A resolution structure of BfrB (D34F) 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 4TOD · PDBe 4TOD · UniProt Q9HY79
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