MolNFT v1 · #170425 · protein
Pseudomonas stutzeri nitrous oxide reductase mutant, H326A
6Y77 · Nitrous-oxide reductase: “Pseudomonas stutzeri nitrous oxide reductase mutant, H326A”. X-ray diffraction, 3 ligands (CUA, ZN, NA), 11 pockets (best druggability 0.81). MolNFT v1 #170425 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Y77
- Type
- protein
- Length
- 1,147 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, ZN, NA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 566 | 12% helix, 44% strand | P19573 |
| B | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 581 | 11% helix, 42% strand | P19573 |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 7 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.81 | 0.92 | 48 | empty |
| 2 | 79 | 0.73 | 0.97 | 26 | empty |
| 3 | 290 | 0.72 | 0.85 | 46 | empty |
| 4 | 146 | 0.44 | 0.76 | 24 | empty |
| 5 | 166 | 0.44 | 0.75 | 25 | FMT |
Interfaces
1 interface between chains.
- A–B · 5106 Ų buried · 73 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 6Y77 · PDBe 6Y77 · UniProt P19573
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