Research workbench
Recombinant pseudomonas stutzeri nitrous oxide reductase, form II
Analyse Recombinant pseudomonas stutzeri nitrous oxide reductase, form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RKZ
- Type
- protein
- Length
- 1,172 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous-oxide reductase
- EC
- 1.7.2.4
- UniProt
- P19573
- Ligands
- CUZ, CUA, NA, CA, K, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 586 | 11% helix, 42% strand | P19573 |
| B | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 586 | 11% helix, 41% strand | P19573 |
Ligands and binding sites
- CUZ · (mu-4-sulfido)-tetra-nuclear copper ion · ligand · 2 copies · chains A, B
- CUA · Dinuclear copper ion · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- FMT · Formic acid · additive · 9 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.79 | 0.91 | 43 | empty |
| 2 | 178 | 0.44 | 0.74 | 25 | empty |
| 3 | 140 | 0.43 | 0.76 | 22 | empty |
| 4 | 88 | 0.32 | 0.73 | 20 | B3P, FMT |
| 5 | 58 | 0.26 | 0.73 | 15 | B3P |
Interfaces
1 interface between chains.
- A–B · 5870 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 6RKZ · Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II · the same entry in another collection · chain A against A, TM-score 1.00
- P19573 · AlphaFold monomer V2.0 prediction for nitrous-oxide reductase (P19573) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P19573
- Elsewhere: RCSB PDB 6RKZ · PDBe 6RKZ · UniProt P19573
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