Research workbench
Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form with substrate
Analyse Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form with substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SBR
- Type
- protein
- Length
- 4,659 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous-oxide reductase
- EC
- 1.7.99.6
- UniProt
- P19573
- Ligands
- CUA, CUK, CA, K, CL, N2O
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, H | Nitrous-oxide reductase (EC 1.7.99.6) | protein | 581 | 11% helix, 41% strand | P19573 |
| D | Nitrous-oxide reductase (EC 1.7.99.6) | protein | 588 | 10% helix, 41% strand | P19573 |
| G | Nitrous-oxide reductase (EC 1.7.99.6) | protein | 585 | 10% helix, 42% strand | P19573 |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CUK · [4Cu:2S] cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- N2O · Nitrous oxide · ion · 2 copies · chains C, D, G, H
- IMD · Imidazole · additive · 6 copies · chains C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.82 | 0.94 | 43 | empty |
| 2 | 261 | 0.81 | 0.93 | 45 | empty |
| 3 | 273 | 0.80 | 0.92 | 45 | empty |
| 4 | 388 | 0.77 | 0.87 | 56 | empty |
| 5 | 1142 | 0.72 | 0.76 | 104 | empty |
Interfaces
12 interfaces between chains.
- G–H · 5881 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 5867 Ų buried · 71 hydrogen bonds · protein-protein
- C–D · 5860 Ų buried · 71 hydrogen bonds · protein-protein
- E–F · 5804 Ų buried · 72 hydrogen bonds · protein-protein
- D–E · 454 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3SBR · Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form with substrate · the same entry in another collection · chain H against H, TM-score 1.00
- P19573 · AlphaFold monomer V2.0 prediction for nitrous-oxide reductase (P19573) · 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 P19573
- Elsewhere: RCSB PDB 3SBR · PDBe 3SBR · UniProt P19573
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