Research workbench
Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96K AB5
Analyse Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDF
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Escherichia coli
- Molecule
- engineered cyt cb 562 variant, C96K AB5
- Ligands
- HEC, ZN, CL
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · resolution 2.35 · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | engineered cyt cb 562 variant, C96K AB5 | protein | 106 | 79% helix, 0% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 8 copies · chains A, C
- CL · Chloride ion · ion · 4 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.54 | 0.87 | 13 | HEC |
| 2 | 68 | 0.50 | 0.84 | 15 | HEC |
| 3 | 57 | 0.41 | 0.81 | 11 | empty |
| 4 | 68 | 0.38 | 0.78 | 12 | HEC |
Interfaces
1 interface between chains.
- A–C · 800 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 6LDF · Crystal structure of the zn-directed tetramer of the engineered cyt cb 562 variant, C96K… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6LDF · PDBe 6LDF
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