MolNFT v1 · #80162 · protein
Crystal structure of an engineered cytochrome CB562 that forms 1D, zn- mediated coordination polymers
3TOL · Soluble cytochrome B562: “Crystal structure of an engineered cytochrome CB562 that forms 1D, zn- mediated coordination polymers”. X-ray diffraction, 3 ligands (HEM, ZN, CA), 8 pockets (best druggability 0.84). MolNFT v1 #80162 on…
- PDB
- 3TOL
- 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, CA
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, B | Soluble cytochrome B562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, D, B
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.84 | 0.85 | 123 | HEM |
| 2 | 397 | 0.61 | 0.77 | 54 | empty |
| 3 | 160 | 0.59 | 0.82 | 26 | HEM |
| 4 | 146 | 0.58 | 0.82 | 21 | HEM |
| 5 | 144 | 0.56 | 0.82 | 21 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 730 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 672 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 233 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 150 Ų buried · 1 hydrogen bond · protein-protein
- D–B · 145 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme attachment).
Compared structures
- 3TOL · Crystal structure of an engineered cytochrome cb562 that forms 1D, Zn-mediated… · the same entry in another collection · chain B against B, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain D 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 3TOL · PDBe 3TOL · UniProt P0ABE7
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