MolNFT v1 · #146963 · protein
MN(II)-bound structure of the engineered cyt CB562 variant, CH2EY
6DY8 · Soluble cytochrome B562: “MN(II)-bound structure of the engineered cyt CB562 variant, CH2EY”. X-ray diffraction, 2 ligands (HEC, MN), 5 pockets (best druggability 0.77). MolNFT v1 #146963 on GenesisL1: 3D structure, binding sites…
- PDB
- 6DY8
- 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
- HEC, MN
- Pockets
- 5 · best druggability 0.77
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
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.77 | 0.80 | 89 | HEC |
| 2 | 243 | 0.72 | 0.87 | 33 | HEC |
| 3 | 126 | 0.59 | 0.84 | 23 | HEC |
| 4 | 152 | 0.59 | 0.83 | 22 | HEC |
| 5 | 165 | 0.54 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 737 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 513 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 6DY8 · Mn(II)-bound structure of the engineered cyt cb562 variant, CH2EY · 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 C against A, TM-score 0.98
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 6DY8 · PDBe 6DY8 · UniProt P0ABE7
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