Research workbench
Crystal structure of nitrous oxide reductase from pseudomonas nautica, at 2.4A resolution
Analyse Crystal structure of nitrous oxide reductase from pseudomonas nautica, at 2.4A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QNI
- Type
- protein
- Length
- 3,432 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous-oxide reductase
- Ligands
- CUA, CUZ, CA, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nitrous-oxide reductase | protein | 572 | 11% helix, 42% strand | — |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 6 copies · chains A, B, C, D, E, F
- CUZ · (mu-4-sulfido)-tetra-nuclear copper ion · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.76 | 0.87 | 44 | empty |
| 2 | 372 | 0.76 | 0.87 | 46 | empty |
| 3 | 362 | 0.74 | 0.85 | 46 | empty |
| 4 | 620 | 0.64 | 0.75 | 56 | empty |
| 5 | 342 | 0.58 | 0.76 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 5971 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 5944 Ų buried · 70 hydrogen bonds · protein-protein
- E–F · 5900 Ų buried · 70 hydrogen bonds · protein-protein
- A–F · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 69 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1QNI · Crystal Structure of Nitrous Oxide Reductase from Pseudomonas nautica, at 2.4A Resolution · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1QNI · PDBe 1QNI
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