Research workbench
Crystal structure of nitric oxide reductase
Analyse Crystal structure of 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
- 3AYF
- Type
- protein
- Length
- 754 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide reductase
- UniProt
- B3Y963
- Ligands
- HEM, LOP, ZN, CA
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide reductase | protein | 754 | 69% helix, 4% strand | B3Y963 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A
- LOP · (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(dodecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.88 | 0.89 | 120 | HEM, ZN, CA, LOP |
| 2 | 229 | 0.82 | 0.94 | 30 | empty |
| 3 | 78 | 0.56 | 0.87 | 17 | empty |
| 4 | 57 | 0.56 | 0.88 | 12 | empty |
| 5 | 218 | 0.51 | 0.76 | 29 | empty |
Compared structures
- 3AYF · Crystal structure of nitric oxide reductase · the same entry in another collection · chain A 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 B3Y963
- Elsewhere: RCSB PDB 3AYF · PDBe 3AYF · UniProt B3Y963
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