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Crystal structure of a dimeric cytochrome CB562 assembly induced by copper coordination
Analyse Crystal structure of a dimeric cytochrome CB562 assembly induced by copper… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DE8
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, CA, CU
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 6 copies · chains A, C, B
- CU · Copper (II) ion · metal · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.87 | 0.88 | 122 | CA |
| 2 | 231 | 0.63 | 0.82 | 34 | HEM |
| 3 | 176 | 0.59 | 0.82 | 31 | empty |
| 4 | 161 | 0.58 | 0.82 | 23 | HEM |
| 5 | 137 | 0.58 | 0.83 | 21 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 483 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 459 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 437 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 376 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 218 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme attachment).
Compared structures
- 3DE8 · Crystal Structure of a Dimeric Cytochrome cb562 Assembly Induced by Copper Coordination · 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 B 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 3DE8 · PDBe 3DE8 · UniProt P0ABE7
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