Research workbench
The structure of cu-nitrite reductase from achromobacter cycloclastes at five pH values, with nitrite bound and with type II cu depleted
Analyse The structure of cu-nitrite reductase from achromobacter cycloclastes at five… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NIB
- Type
- protein
- Length
- 999 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.99.3
- UniProt
- P25006
- Ligands
- CU
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nitrite reductase (EC 1.7.99.3) | protein | 333 | 10% helix, 41% strand | P25006 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.83 | 0.95 | 32 | empty |
| 2 | 510 | 0.81 | 0.88 | 54 | empty |
| 3 | 104 | 0.77 | 0.97 | 19 | empty |
| 4 | 98 | 0.77 | 0.97 | 20 | empty |
| 5 | 90 | 0.76 | 0.97 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2146 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2132 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1929 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1NIB · The structure of cu-nitrite reductase from achromobacter cycloclastes at five pH values… · the same entry in another collection · chain A against A, TM-score 1.00
- P25006 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P25006) · a predicted model of the same protein · chain A 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 P25006
- Elsewhere: RCSB PDB 1NIB · PDBe 1NIB · UniProt P25006
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.