Research workbench
Pseudomonas stutzeri nitrous oxide reductase mutant, H494A
Analyse Pseudomonas stutzeri nitrous oxide reductase mutant, H494A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y7E
- Type
- protein
- Length
- 1,160 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, CA, CL
- Pockets
- 8 · best druggability 0.81
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 | 572 | 11% helix, 43% strand | P19573 |
| B | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 588 | 11% helix, 41% strand | P19573 |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 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 · 4 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
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.81 | 0.92 | 45 | empty |
| 2 | 64 | 0.71 | 0.97 | 22 | ZN |
| 3 | 162 | 0.45 | 0.75 | 26 | empty |
| 4 | 163 | 0.45 | 0.75 | 26 | FMT |
| 5 | 144 | 0.44 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 5564 Ų buried · 70 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 6Y7E · PDBe 6Y7E · UniProt P19573
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