Research workbench
Cu-bound crystal structure of the engineered cyt CB562 variant, DICYT2 - H63A, crystallized in the presence of CU(II)
Analyse Cu-bound crystal structure of the engineered cyt CB562 variant, DICYT2 - H63A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LSJ
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEC, CA, CU
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains C, A
- CA · Calcium ion · metal · 5 copies · chains C, A
- CU · Copper (II) ion · metal · chains C, A
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 | 407 | 0.69 | 0.81 | 45 | HEC |
| 2 | 155 | 0.63 | 0.84 | 22 | HEC |
| 3 | 73 | 0.36 | 0.77 | 15 | empty |
| 4 | 82 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- C–A · 586 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 disulfide (heme c attachment, disulfide).
Compared structures
- 7LSJ · Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A… · the same entry in another collection · chain C against C, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 7LSJ · PDBe 7LSJ · UniProt P0ABE7
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