MolNFT v1 · #154217 · protein
Cryo-EM structure of apo-bacterioferritin from streptomyces coelicolor
6K3O: “Cryo-EM structure of apo-bacterioferritin from streptomyces coelicolor”. Electron microscopy, 2 ligands (HEM, FE2), 20 pockets (best druggability 0.77). MolNFT v1 #154217 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K3O
- Type
- protein
- Length
- 3,790 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 0.77
Structure
electron microscopy · 3 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, I, L, O, Q, V | Bacterioferritin (EC 1.16.3.1) | protein | 158 | 74% helix, 0% strand | Q9S2N0 |
| B, D, K, M, P, R, T, U, W | Bacterioferritin (EC 1.16.3.1) | protein | 157 | 75% helix, 1% strand | Q9S2N0 |
| F, G, H, J, N, S, X | Bacterioferritin (EC 1.16.3.1) | protein | 159 | 74% 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 | 327 | 0.77 | 0.88 | 29 | HEM |
| 2 | 318 | 0.77 | 0.88 | 29 | HEM |
| 3 | 329 | 0.76 | 0.87 | 30 | HEM |
| 4 | 322 | 0.76 | 0.87 | 29 | HEM |
| 5 | 349 | 0.76 | 0.86 | 31 | HEM |
Interfaces
60 interfaces between chains.
- C–D · 929 Ų buried · 3 hydrogen bonds · protein-protein
- F–E · 921 Ų buried · 3 hydrogen bonds · protein-protein
- G–X · 917 Ų buried · 4 hydrogen bonds · protein-protein
- J–K · 916 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 914 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 cofactor (heme attachment).
Compared structures
- 6K3O · Cryo-EM structure of Apo-bacterioferritin from Streptomyces coelicolor · the same entry in another collection · chain K against K, 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 6K3O · PDBe 6K3O · UniProt Q9S2N0
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