Research workbench
Crystal structure of nitrous oxide reductase from P. denitrificans
Analyse Crystal structure of nitrous oxide reductase from P. denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FWX
- Type
- protein
- Length
- 2,358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous oxide reductase
- EC
- 1.7.99.6
- UniProt
- Q51705
- Ligands
- CUA, CUZ, CA, CL
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrous oxide reductase (EC 1.7.99.6) | protein | 591 | 12% helix, 42% strand | Q51705 |
| B | Nitrous oxide reductase (EC 1.7.99.6) | protein | 589 | 13% helix, 42% strand | Q51705 |
| C | Nitrous oxide reductase (EC 1.7.99.6) | protein | 590 | 14% helix, 42% strand | Q51705 |
| D | Nitrous oxide reductase (EC 1.7.99.6) | protein | 588 | 13% helix, 42% strand | Q51705 |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 4 copies · chains A, B, C, D
- CUZ · (mu-4-sulfido)-tetra-nuclear copper ion · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.80 | 0.93 | 46 | empty |
| 2 | 275 | 0.79 | 0.91 | 47 | empty |
| 3 | 97 | 0.78 | 0.99 | 23 | empty |
| 4 | 99 | 0.78 | 0.98 | 23 | empty |
| 5 | 84 | 0.78 | 0.99 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6371 Ų buried · 107 hydrogen bonds · protein-protein
- C–D · 6316 Ų buried · 101 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1FWX · Crystal structure of nitrous oxide reductase from P. denitrificans · the same entry in another collection · chain D against D, TM-score 1.00
- Q51705 · AlphaFold monomer V2.0 prediction for nitrous-oxide reductase (Q51705) · a predicted model of the same protein · chain B 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 Q51705
- Elsewhere: RCSB PDB 1FWX · PDBe 1FWX · UniProt Q51705
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