MolNFT v1 · #170431 · protein
Pseudomonas stutzeri nitrous oxide reductase mutant, H433A
6Y7D · Nitrous-oxide reductase: “Pseudomonas stutzeri nitrous oxide reductase mutant, H433A”. X-ray diffraction, 4 ligands (CUA, NA, CA), 6 pockets (best druggability 0.78). MolNFT v1 #170431 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Y7D
- Type
- protein
- Length
- 1,158 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, CL
- Pockets
- 6 · best druggability 0.78
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 | 588 | 12% 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, B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 6 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 | 257 | 0.78 | 0.91 | 40 | empty |
| 2 | 133 | 0.50 | 0.79 | 28 | empty |
| 3 | 184 | 0.46 | 0.75 | 26 | FMT |
| 4 | 158 | 0.45 | 0.76 | 26 | empty |
| 5 | 73 | 0.30 | 0.73 | 17 | B3P, FMT |
Interfaces
1 interface between chains.
- A–B · 5577 Ų buried · 78 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
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 6Y7D · PDBe 6Y7D · UniProt P19573
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