MolNFT v1 · #140275 · protein
Time-resolved sfx structure of cytochrome P450NOR: dark-2 data in the presence of NADH (resting state)
5Y5J · NADP nitrous oxide-forming nitric oxide reductase: “Time-resolved sfx structure of cytochrome P450NOR: dark-2 data in the presence of NADH (resting state)”. X-ray diffraction, 1 ligand (HEM), 6 pockets (best druggability 0.83).…
- PDB
- 5Y5J
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP nitrous oxide-forming nitric oxide reductase
- EC
- 1.7.1.14
- UniProt
- P23295
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADP nitrous oxide-forming nitric oxide reductase (EC 1.7.1.14) | protein | 399 | 52% helix, 10% strand | P23295 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.83 | 0.84 | 91 | HEM, GOL |
| 2 | 1038 | 0.80 | 0.82 | 84 | HEM, GOL |
| 3 | 383 | 0.56 | 0.74 | 42 | empty |
| 4 | 65 | 0.32 | 0.75 | 12 | empty |
| 5 | 58 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5Y5J · Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH… · the same entry in another collection · chain A against A, TM-score 1.00
- P23295 · AlphaFold monomer V2.0 prediction for NADP nitrous oxide-forming nitric oxide reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P23295
- Elsewhere: RCSB PDB 5Y5J · PDBe 5Y5J · UniProt P23295
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