Research workbench
Cryo-EM structure of holo-bacterioferritin-form-I from streptomyces coelicolor
Analyse Cryo-EM structure of holo-bacterioferritin-form-I from streptomyces coelicolor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K43
- Type
- protein
- Length
- 3,840 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- EC
- 1.16.3.1
- UniProt
- Q9S2N0
- Ligands
- HEM, FE2
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, J, L, O, Q, T, V | Bacterioferritin (EC 1.16.3.1) | protein | 162 | 73% helix, 1% strand | Q9S2N0 |
| B, D, K, M, P, R, U, W | Bacterioferritin (EC 1.16.3.1) | protein | 157 | 77% helix, 1% strand | Q9S2N0 |
| F, E, G, H, I, N, S, X | Bacterioferritin (EC 1.16.3.1) | protein | 161 | 75% helix, 1% strand | Q9S2N0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, F, E, J, K, L, M, H, N, O, P, Q, R, I, S, T, U, V, W, G, X
- FE2 · Fe (II) ion · metal · 24 copies · chains A, B, C, D, F, E, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
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 | 339 | 0.76 | 0.87 | 27 | HEM |
| 2 | 333 | 0.76 | 0.87 | 30 | HEM |
| 3 | 305 | 0.75 | 0.87 | 30 | HEM |
| 4 | 303 | 0.75 | 0.87 | 31 | HEM |
| 5 | 322 | 0.75 | 0.86 | 29 | HEM |
Interfaces
60 interfaces between chains.
- G–X · 1073 Ų buried · 6 hydrogen bonds · protein-protein
- F–E · 1072 Ų buried · 10 hydrogen bonds · protein-protein
- I–S · 1067 Ų buried · 6 hydrogen bonds · protein-protein
- H–N · 1064 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1058 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 cofactor (heme attachment).
Compared structures
- 6K43 · Cryo-EM structure of Holo-bacterioferritin-form-I from Streptomyces coelicolor · the same entry in another collection · chain I against I, 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 Q9S2N0
- Elsewhere: RCSB PDB 6K43 · PDBe 6K43 · UniProt Q9S2N0
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