Research workbench
Crystal structure of the complex of lactoperoxidase with nitric oxide at 2.50A resolution
Analyse Crystal structure of the complex of lactoperoxidase with nitric oxide at 2.50A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y3U
- Type
- protein
- Length
- 1,190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- L8ICE9
- Ligands
- MH0, NAG, BMA, CA, NO, CL
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 10% strand | L8ICE9 |
Ligands and binding sites
- MH0 · Mesoheme · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- NO · Nitric oxide · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.86 | 0.87 | 115 | MH0, NO |
| 2 | 1179 | 0.83 | 0.83 | 103 | ACT, MH0, NO |
| 3 | 515 | 0.66 | 0.77 | 60 | empty |
| 4 | 503 | 0.65 | 0.77 | 67 | empty |
| 5 | 146 | 0.46 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1050 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 9 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7Y3U · Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution · 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 L8ICE9
- Elsewhere: RCSB PDB 7Y3U · PDBe 7Y3U · UniProt L8ICE9
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