Research workbench
Structure of nitrite bound to oxidized alcaligenes faecalis nitrite reductase at cryo temperature
Analyse Structure of nitrite bound to oxidized alcaligenes faecalis nitrite reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AS6
- Type
- protein
- Length
- 1,006 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.99.3
- UniProt
- P38501
- Ligands
- CU, NO2
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrite reductase (EC 1.7.99.3) | protein | 335 | 10% helix, 43% strand | P38501 |
| B | Nitrite reductase (EC 1.7.99.3) | protein | 336 | 11% helix, 42% strand | P38501 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
- NO2 · Nitrite ion · ion · 3 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.84 | 0.96 | 30 | empty |
| 2 | 522 | 0.80 | 0.87 | 60 | empty |
| 3 | 68 | 0.75 | 0.99 | 17 | empty |
| 4 | 65 | 0.74 | 0.98 | 18 | empty |
| 5 | 55 | 0.71 | 0.98 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2110 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2106 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2098 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1AS6 · Structure of nitrite bound to oxidized alcaligenes faecalis nitrite reductase at cryo… · the same entry in another collection · chain A against A, TM-score 1.00
- P38501 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P38501) · a predicted model of the same protein · 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 P38501
- Elsewhere: RCSB PDB 1AS6 · PDBe 1AS6 · UniProt P38501
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