MolNFT v1 · #173133 · protein
Pseudomonas stutzeri nitrous oxide reductase mutant, D576A
7APY · Nitrous-oxide reductase: “Pseudomonas stutzeri nitrous oxide reductase mutant, D576A”. X-ray diffraction, 6 ligands (CUZ, CUA, NA), 6 pockets (best druggability 0.79). MolNFT v1 #173133 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7APY
- 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
- 6 · 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, 43% 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.79 | 0.91 | 43 | empty |
| 2 | 180 | 0.44 | 0.74 | 26 | empty |
| 3 | 161 | 0.44 | 0.75 | 24 | empty |
| 4 | 86 | 0.33 | 0.73 | 20 | B3P, FMT |
| 5 | 68 | 0.31 | 0.75 | 20 | NA |
Interfaces
1 interface between chains.
- A–B · 5889 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 7APY · PDBe 7APY · UniProt P19573
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