MolNFT v1 · #154236 · protein
Cryo-EM structure of holo-bacterioferritin form-II from streptomyces coelicolor
6K4M: “Cryo-EM structure of holo-bacterioferritin form-II from streptomyces coelicolor”. Electron microscopy, 2 ligands (HEM, FE2), 20 pockets (best druggability 0.85). MolNFT v1 #154236 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6K4M
- 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 0.85
Structure
electron microscopy · 3 distinct chains · 75% helix, 0% 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 | 76% helix, 0% strand | Q9S2N0 |
| B, D, K, M, P, R, T, U, W | Bacterioferritin (EC 1.16.3.1) | protein | 157 | 76% helix, 0% 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, H, N, J, K, L, M, 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 | 1031 | 0.85 | 0.86 | 147 | empty |
| 2 | 886 | 0.85 | 0.86 | 131 | empty |
| 3 | 756 | 0.84 | 0.86 | 100 | empty |
| 4 | 1048 | 0.81 | 0.83 | 128 | empty |
| 5 | 340 | 0.81 | 0.91 | 61 | empty |
Interfaces
60 interfaces between chains.
- C–D · 826 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 10 hydrogen bonds · protein-protein
- I–S · 815 Ų buried · 9 hydrogen bonds · protein-protein
- F–E · 813 Ų buried · 8 hydrogen bonds · protein-protein
- G–X · 813 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 cofactor (heme attachment).
Compared structures
- 6K4M · Cryo-EM structure of Holo-bacterioferritin form-II 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 6K4M · PDBe 6K4M · UniProt Q9S2N0
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