Research workbench
Crystal structure of nitric oxide reductase from pseudomonas aeruginosa in complex with antibody fragment
Analyse Crystal structure of nitric oxide reductase from pseudomonas aeruginosa in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O0R
- 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
- 1.7.99.7
- UniProt
- Q59647, Q59646
- Ligands
- HEM, HEC, FE, CA, O
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 46% 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 | 7% helix, 51% strand | — |
| B | Nitric oxide reductase subunit B (EC 1.7.99.7) | protein | 449 | 79% helix, 0% strand | Q59647 |
| C | Nitric oxide reductase subunit C (EC 1.7.99.7) | protein | 142 | 60% helix, 4% strand | Q59646 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C
- HEC · Heme C · ligand · chains B, C
- FE · Fe (III) ion · metal · chains B
- CA · Calcium ion · metal · chains B, C
- O · Oxygen atom · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.88 | 0.93 | 74 | HEM, O |
| 2 | 713 | 0.80 | 0.84 | 75 | HEC |
| 3 | 60 | 0.72 | 0.98 | 15 | empty |
| 4 | 72 | 0.69 | 0.94 | 25 | empty |
| 5 | 194 | 0.54 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3431 Ų buried · 48 hydrogen bonds · protein-protein
- L–H · 1930 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 395 Ų buried · 5 hydrogen bonds · protein-protein
- L–C · 277 Ų buried · 2 hydrogen bonds · protein-protein
- H–C · 209 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 cofactor (disulfide, heme c attachment).
Compared structures
- 3O0R · Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with… · 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 3O0R · PDBe 3O0R · UniProt Q59647 · UniProt Q59646
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