Research workbench
Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin
Analyse Crystal structure of the electron-transfer complex of copper nitrite reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B1J
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Alcaligenes xylosoxydans xylosoxydans; Hyphomicrobium denitrificans
- Molecule
- Copper-containing nitrite reductase; Blue copper protein
- EC
- 1.7.2.1
- UniProt
- O68601, A7VL37
- Ligands
- CU
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · resolution 3 · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 334 | 10% helix, 40% strand | O68601 |
| C | Blue copper protein | protein | 124 | 19% helix, 37% strand | A7VL37 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.81 | 0.84 | 73 | empty |
| 2 | 103 | 0.52 | 0.83 | 27 | empty |
| 3 | 106 | 0.51 | 0.82 | 19 | empty |
| 4 | 94 | 0.42 | 0.78 | 22 | empty |
| 5 | 65 | 0.33 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 399 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 340 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5B1J · Crystal structure of the electron-transfer complex of copper nitrite reductase with a… · the same entry in another collection · chain A against A, 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 O68601
- Every structure of UniProt A7VL37
- Elsewhere: RCSB PDB 5B1J · PDBe 5B1J · UniProt O68601 · UniProt A7VL37
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