MolNFT v1 · #142866 · protein
Disulfide-free, zn-directed tetramer of the engineered cyt CB562 variant, C96T/A104AB3
6AI5 · Soluble cytochrome B562: “Disulfide-free, zn-directed tetramer of the engineered cyt CB562 variant, C96T/A104AB3”. X-ray diffraction, 4 ligands (HEM, ZN, MG), 8 pockets (best druggability 0.88). MolNFT v1 #142866 on GenesisL1: 3D…
- PDB
- 6AI5
- 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, ZN, MG, CL
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Soluble cytochrome B562 | protein | 106 | 82% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, E, G
- ZN · Zinc ion · metal · 8 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
- CL · Chloride ion · ion · 5 copies · chains A, G, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.88 | 0.90 | 126 | CL |
| 2 | 161 | 0.59 | 0.82 | 22 | HEM |
| 3 | 152 | 0.58 | 0.82 | 25 | HEM |
| 4 | 149 | 0.57 | 0.82 | 27 | HEM |
| 5 | 157 | 0.56 | 0.81 | 25 | HEM |
Interfaces
6 interfaces between chains.
- A–C · 797 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 771 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 594 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 554 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 267 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme attachment).
Compared structures
- 6AI5 · Disulfide-free, Zn-directed tetramer of the engineered cyt cb562 variant, C96T/A104AB3 · the same entry in another collection · chain G against G, 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 6AI5 · PDBe 6AI5 · UniProt P0ABE7
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