Research workbench
Crystal structure of an engineered protein that forms nanotubes with tunable diameters
Analyse Crystal structure of an engineered protein that forms nanotubes with tunable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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