MolNFT v1 · #73394 · protein
Crystal structure of nitric oxide reductase from pseudomonas aeruginosa in complex with antibody fragment
3O0R · Antibody Fab fragment light chain: “Crystal structure of nitric oxide reductase from pseudomonas aeruginosa in complex with antibody fragment”. X-ray diffraction, 5 ligands (HEM, HEC, FE), 12 pockets (best druggability 0.88). MolNFT…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.