Research workbench
A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form
Analyse A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FOO
- Type
- protein
- Length
- 1,272 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Escherichia coli
- Molecule
- Soluble cytochrome b562
- UniProt
- P0ABE7
- Ligands
- HEM, PXX, NI
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Soluble cytochrome b562 | protein | 106 | 79% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PXX · N-1,10-phenanthrolin-5-ylacetamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, L, K
- NI · Nickel (II) ion · metal · 24 copies · chains A, B, C, D, F, E, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.68 | 0.79 | 50 | empty |
| 2 | 484 | 0.67 | 0.78 | 59 | empty |
| 3 | 382 | 0.64 | 0.79 | 40 | empty |
| 4 | 164 | 0.59 | 0.82 | 24 | HEM |
| 5 | 179 | 0.59 | 0.81 | 22 | HEM |
Interfaces
27 interfaces between chains.
- B–F · 257 Ų buried · 1 hydrogen bond · protein-protein
- F–H · 252 Ų buried · 4 hydrogen bonds · protein-protein
- E–I · 252 Ų buried · 4 hydrogen bonds · protein-protein
- D–G · 251 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 247 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 23 cofactor, 11 covalent (heme attachment, covalent ligand).
Compared structures
- 3FOO · A triangular cytochrome B562 superstructure mediated by ni coordination - monoclinic form · the same entry in another collection · chain L against L, TM-score 1.00
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 3FOO · PDBe 3FOO · UniProt P0ABE7
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