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The 2.6 a structure resolution of rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic special position
Analyse The 2.6 a structure resolution of rhodobacter capsulatus bacterioferritin with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JGC
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- UniProt
- Q59738
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bacterioferritin | protein | 160 | 78% helix, 0% strand | Q59738 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.55 | 0.87 | 19 | empty |
| 2 | 62 | 0.53 | 0.87 | 18 | empty |
| 3 | 71 | 0.52 | 0.86 | 19 | empty |
| 4 | 52 | 0.27 | 0.74 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–B · 419 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 419 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 416 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1JGC · The 2.6 A Structure Resolution of Rhodobacter capsulatus Bacterioferritin with Metal-free… · the same entry in another collection · chain A against A, TM-score 1.00
- Q59738 · AlphaFold monomer V2.0 prediction for bacterioferritin (Q59738) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q59738
- Elsewhere: RCSB PDB 1JGC · PDBe 1JGC · UniProt Q59738
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