MolNFT v1 · #31966 · protein
Crystal structure of E. COLI cytochrome B562 with engineered C-type heme linkages
2BC5 · Soluble cytochrome B562: “Crystal structure of E. COLI cytochrome B562 with engineered C-type heme linkages”. X-ray diffraction, 2 ligands (HEC, SO4), 7 pockets (best druggability 0.78). MolNFT v1 #31966 on GenesisL1: 3D structure…
- PDB
- 2BC5
- 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, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.78 | 0.80 | 77 | empty |
| 2 | 152 | 0.59 | 0.82 | 23 | HEC |
| 3 | 176 | 0.58 | 0.81 | 24 | HEC |
| 4 | 163 | 0.58 | 0.81 | 23 | HEC |
| 5 | 151 | 0.58 | 0.82 | 19 | HEC |
Interfaces
5 interfaces between chains.
- C–D · 811 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 804 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 418 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 402 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 2BC5 · Crystal structure of E. coli cytochrome b562 with engineered c-type heme linkages · 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 0.98
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 2BC5 · PDBe 2BC5 · UniProt P0ABE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.