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
- 1NIA
- 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
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nitrite reductase (EC 1.7.99.3) | protein | 333 | 10% helix, 42% 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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.83 | 0.95 | 30 | empty |
| 2 | 516 | 0.81 | 0.88 | 53 | empty |
| 3 | 101 | 0.78 | 0.98 | 21 | empty |
| 4 | 94 | 0.76 | 0.97 | 20 | empty |
| 5 | 87 | 0.76 | 0.98 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2148 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2122 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1927 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1NIA · The structure of cu-nitrite reductase from achromobacter cycloclastes at five pH values… · the same entry in another collection · chain C against C, 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 1NIA · PDBe 1NIA · UniProt P25006
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