MolNFT v1 · #170420 · protein
Pseudomonas stutzeri nitrous oxide reductase mutant, H178A
6Y72 · Nitrous-oxide reductase: “Pseudomonas stutzeri nitrous oxide reductase mutant, H178A”. X-ray diffraction, 5 ligands (CUA, NA, CA), 8 pockets (best druggability 0.80). MolNFT v1 #170420 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Y72
- Type
- protein
- Length
- 1,171 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, CA, K, CL
- Pockets
- 8 · best druggability 0.80
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 | 585 | 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
- CUA · Dinuclear copper ion · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains A, B
- CL · Chloride ion · ion · chains A
- 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.80 | 0.92 | 45 | empty |
| 2 | 65 | 0.74 | 0.99 | 25 | empty |
| 3 | 68 | 0.73 | 0.98 | 22 | empty |
| 4 | 159 | 0.44 | 0.75 | 25 | NA |
| 5 | 149 | 0.43 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 5826 Ų buried · 77 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 6Y72 · PDBe 6Y72 · UniProt P19573
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