MolNFT v1 · #19546 · protein
Crystal structure of nitrous oxide reductase from pseudomonas nautica, at 2.4A resolution
1QNI · Nitrous-oxide reductase: “Crystal structure of nitrous oxide reductase from pseudomonas nautica, at 2.4A resolution”. X-ray diffraction, 4 ligands (CUA, CUZ, CA), 20 pockets (best druggability 0.76). MolNFT v1 #19546 on GenesisL1…
- 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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