MolNFT v1 · #83348 · protein
Reduced and cyanide-bound cytochrome C-dependent nitric oxide reductase (cnor) from pseudomonas aeruginosa in complex with antibody fragment
3WFE · Antibody Fab fragment light chain: “Reduced and cyanide-bound cytochrome C-dependent nitric oxide reductase (cnor) from pseudomonas aeruginosa in…”. X-ray diffraction, 6 ligands (HEM, 10M, HEC), 13 pockets (best druggability 0.89).…
- PDB
- 3WFE
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; Antibody Fab fragment heavy chain; Nitric oxide…
- EC
- 1.7.2.5
- UniProt
- Q59647, Q59646
- Ligands
- HEM, 10M, HEC, FE, CA, CYN
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody Fab fragment light chain | protein | 213 | 6% helix, 54% strand | — |
| H | Antibody Fab fragment heavy chain | protein | 225 | 7% helix, 50% strand | — |
| B | Nitric oxide reductase subunit B (EC 1.7.2.5) | protein | 449 | 78% helix, 0% strand | Q59647 |
| C | Nitric oxide reductase subunit C | protein | 142 | 59% helix, 3% strand | Q59646 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C
- 10M · decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside · ligand · 2 copies · chains B, C
- HEC · Heme C · ligand · chains H, B, C
- FE · Fe (III) ion · metal · chains B
- CA · Calcium ion · metal · chains B, C
- CYN · Cyanide ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.89 | 0.93 | 79 | HEM, CYN, CA |
| 2 | 689 | 0.79 | 0.83 | 78 | HEC |
| 3 | 63 | 0.72 | 0.98 | 15 | empty |
| 4 | 65 | 0.65 | 0.92 | 19 | empty |
| 5 | 372 | 0.55 | 0.74 | 57 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3425 Ų buried · 48 hydrogen bonds · protein-protein
- L–H · 1932 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 392 Ų buried · 5 hydrogen bonds · protein-protein
- L–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
- H–C · 199 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 cofactor (disulfide, heme c attachment).
Compared structures
- 3WFE · Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from… · the same entry in another collection · chain L against L, 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 3WFE · PDBe 3WFE · UniProt Q59647 · UniProt Q59646
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