Research workbench
Inhibitor-bound form of nitrous oxide reductase from achromobacter cycloclastes at 1.7 ångström resolution
Analyse Inhibitor-bound form of nitrous oxide reductase from achromobacter cycloclastes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IWK
- Type
- protein
- Length
- 1,180 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous oxide reductase
- EC
- 1.7.99.6
- UniProt
- P94127
- Ligands
- CUZ, NA, CA, CU, IOD, CL
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrous oxide reductase (EC 1.7.99.6) | protein | 590 | 13% helix, 41% strand | P94127 |
Ligands and binding sites
- CUZ · (mu-4-sulfido)-tetra-nuclear copper ion · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 30 copies · chains A, B
- CA · Calcium ion · metal · 28 copies · chains A, B
- CU · Copper (II) ion · metal · 4 copies · chains A, B
- IOD · Iodide ion · ion · 15 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.76 | 0.85 | 64 | CA, CL, NA |
| 2 | 305 | 0.76 | 0.88 | 46 | CA |
| 3 | 80 | 0.76 | 0.98 | 23 | empty |
| 4 | 57 | 0.71 | 0.98 | 17 | CA, NA |
| 5 | 109 | 0.61 | 0.87 | 30 | CA |
Interfaces
1 interface between chains.
- A–B · 6364 Ų buried · 102 hydrogen bonds · protein-protein
Compared structures
- 2IWK · Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7… · the same entry in another collection · chain A against A, TM-score 1.00
- P94127 · AlphaFold monomer V2.0 prediction for nitrous-oxide reductase (P94127) · a predicted model of the same protein · 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
- Every structure of UniProt P94127
- Elsewhere: RCSB PDB 2IWK · PDBe 2IWK · UniProt P94127
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.