Research workbench
Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment
Analyse Reduced and acetaldoxime-bound cytochrome c-dependent nitric oxide reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WFD
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mus musculus; Pseudomonas aeruginosa
- Molecule
- antibody fab fragment light chain; antibody fab fragment heavy chain; Nitric oxide…
- EC
- 1.7.2.5
- UniProt
- Q59647, Q59646
- Ligands
- HEM, AXO, HEC, 10M, FE, CA
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | antibody fab fragment light chain | protein | 213 | 6% helix, 51% strand | — |
| H | antibody fab fragment heavy chain | protein | 225 | 8% helix, 51% strand | — |
| B | Nitric oxide reductase subunit B (EC 1.7.2.5) | protein | 449 | 79% helix, 0% strand | Q59647 |
| C | Nitric oxide reductase subunit C | protein | 142 | 58% helix, 4% strand | Q59646 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C
- AXO · (1E)-N-hydroxyethanimine · ligand · chains B
- HEC · Heme C · ligand · chains H, B, C
- 10M · decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside · sugar · 2 copies · chains B, C
- FE · Fe (III) ion · metal · chains B
- CA · Calcium ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.88 | 0.93 | 64 | HEM, AXO |
| 2 | 645 | 0.80 | 0.84 | 68 | HEC |
| 3 | 145 | 0.78 | 0.95 | 37 | empty |
| 4 | 65 | 0.74 | 0.98 | 15 | empty |
| 5 | 123 | 0.54 | 0.82 | 30 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3427 Ų buried · 50 hydrogen bonds · protein-protein
- L–H · 1953 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 395 Ų buried · 5 hydrogen bonds · protein-protein
- L–C · 291 Ų buried · 2 hydrogen bonds · protein-protein
- H–C · 221 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 cofactor (disulfide, heme c attachment).
Compared structures
- 3WFD · Reduced and acetaldoxime-bound cytochrome C-dependent nitric oxide reductase (cnor) from… · the same entry in another collection · chain B against B, TM-score 1.00
- Q59647 · AlphaFold monomer V2.0 prediction for nitric oxide reductase subunit B (Q59647) · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q59646 · AlphaFold monomer V2.0 prediction for nitric oxide reductase subunit C (Q59646) · a predicted model of the same protein · chain C 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 Q59647
- Every structure of UniProt Q59646
- Elsewhere: RCSB PDB 3WFD · PDBe 3WFD · UniProt Q59647 · UniProt Q59646
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