Research workbench
Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
Analyse Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MK4
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.27
- Source
- Escherichia coli
- Molecule
- Soluble cytochrome b562
- UniProt
- P0ABE7
- Ligands
- HEC, CO
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.27 · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Soluble cytochrome b562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.75 | 0.84 | 57 | HEC |
| 2 | 121 | 0.53 | 0.81 | 20 | HEC |
Interfaces
1 interface between chains.
- A–B · 393 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 7MK4 · Co-bound crystal structure of the engineered cyt CB562 variant, DICYT2 · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 7MK4 · PDBe 7MK4 · UniProt P0ABE7
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