MolNFT v1 · #169292 · protein
Co-bound structure of an engineered protein trimer, TRICYT3, with delta isomerism at the hexahistidine coordination site
6X7E · Soluble cytochrome B562: “Co-bound structure of an engineered protein trimer, TRICYT3, with delta isomerism at the hexahistidine…”. X-ray diffraction, 4 ligands (HEC, MG, CO), 6 pockets (best druggability 0.75). MolNFT v1 #169292 on…
- PDB
- 6X7E
- Type
- protein
- Length
- 318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEC, MG, CO, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B
- CO · Cobalt (II) ion · metal · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
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 | 69 | 0.75 | 0.99 | 16 | CL |
| 2 | 423 | 0.68 | 0.80 | 53 | HEC |
| 3 | 299 | 0.63 | 0.80 | 34 | empty |
| 4 | 264 | 0.62 | 0.80 | 41 | HEC |
| 5 | 147 | 0.57 | 0.82 | 22 | HEC |
Interfaces
3 interfaces between chains.
- A–C · 666 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 648 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (heme c attachment).
Compared structures
- 6X7E · Co-bound structure of an engineered protein trimer, TriCyt3, with delta isomerism at the… · 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 0.97
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 6X7E · PDBe 6X7E · UniProt P0ABE7
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