MolNFT v2 · #195356 · protein
Crystal structure of a Cu-bound cytochrome cb562 variant in the presence of reductant
7TEP · Soluble cytochrome b562: “Crystal structure of a Cu-bound cytochrome cb562 variant in the presence of reductant”. X-ray diffraction at 2.7, 2 ligands (HEC, CU), 6 pockets (best druggability 0.87). MolNFT v2 #195356 on GenesisL1: 3D…
- PDB
- 7TEP
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Escherichia coli
- Molecule
- Soluble cytochrome b562
- UniProt
- P0ABE7
- Ligands
- HEC, CU
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome b562 | protein | 106 | 76% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.87 | 0.92 | 64 | empty |
| 2 | 152 | 0.65 | 0.86 | 22 | HEC |
| 3 | 227 | 0.63 | 0.82 | 28 | HEC |
| 4 | 191 | 0.62 | 0.82 | 37 | HEC |
| 5 | 158 | 0.57 | 0.82 | 30 | HEC |
Interfaces
6 interfaces between chains.
- C–D · 871 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 807 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 709 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 671 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (heme c attachment).
Compared structures
- 7TEP · Crystal structure of a cu-bound cytochrome CB562 variant in the presence of reductant · the same entry in another collection · chain D against D, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A 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 7TEP · PDBe 7TEP · UniProt P0ABE7
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