Research workbench
Pseudomonas stutzeri nitrous oxide reductase mutant, H129A
Analyse Pseudomonas stutzeri nitrous oxide reductase mutant, H129A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y6Y
- Type
- protein
- Length
- 1,156 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
- CUA, NA, ZN, CA, CL
- Pockets
- 7 · 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 | 570 | 11% helix, 43% strand | P19573 |
| B | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 586 | 12% helix, 42% strand | P19573 |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 2 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.79 | 0.90 | 42 | empty |
| 2 | 60 | 0.73 | 0.99 | 21 | empty |
| 3 | 245 | 0.70 | 0.85 | 44 | empty |
| 4 | 158 | 0.45 | 0.76 | 25 | empty |
| 5 | 166 | 0.45 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 5503 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
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 6Y6Y · PDBe 6Y6Y · UniProt P19573
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