Research workbench
Crystal structure of a tetrameric zn-bound cytochrome CB562 complex with covalently and non-covalently stabilized interfaces
Analyse Crystal structure of a tetrameric zn-bound cytochrome CB562 complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IQ6
- Type
- protein
- Length
- 848 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, ZN
- Pockets
- 11 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Soluble cytochrome B562 | protein | 106 | 78% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, E, C, H, D, F, G
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, G, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.89 | 0.90 | 122 | HEM |
| 2 | 1162 | 0.88 | 0.89 | 119 | empty |
| 3 | 1057 | 0.82 | 0.83 | 103 | HEM |
| 4 | 197 | 0.68 | 0.86 | 29 | HEM |
| 5 | 157 | 0.62 | 0.84 | 22 | HEM |
Interfaces
14 interfaces between chains.
- A–B · 796 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 745 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 725 Ų buried · 4 hydrogen bonds · protein-protein
- E–H · 700 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 506 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor, 4 disulfide (heme attachment, disulfide).
Compared structures
- 3IQ6 · Crystal structure of a tetrameric Zn-bound cytochrome cb562 complex with covalently and… · the same entry in another collection · chain H against H, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain G against A, TM-score 0.96
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 P0ABE7
- Elsewhere: RCSB PDB 3IQ6 · PDBe 3IQ6 · UniProt P0ABE7
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