MolNFT v1 · #114589 · protein
Crystal structure of an engineered protein that forms nanotubes with tunable diameters
5BU7 · Soluble cytochrome B562: “Crystal structure of an engineered protein that forms nanotubes with tunable diameters”. X-ray diffraction, 2 ligands (HEM, ZN), 6 pockets (best druggability 0.58). MolNFT v1 #114589 on GenesisL1: 3D…
- PDB
- 5BU7
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HEM, ZN
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Soluble cytochrome B562 | protein | 106 | 78% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.58 | 0.82 | 23 | HEM |
| 2 | 140 | 0.54 | 0.81 | 24 | empty |
| 3 | 113 | 0.52 | 0.82 | 23 | empty |
| 4 | 89 | 0.51 | 0.83 | 18 | HEM |
| 5 | 55 | 0.48 | 0.85 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme attachment).
Compared structures
- 5BU7 · Crystal structure of an engineered protein that forms nanotubes with tunable diameters · 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 5BU7 · PDBe 5BU7 · UniProt P0ABE7
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