Research workbench
Crystal structure of the complex of goat lactoperoxidase with thiocyanate at 3.2 a resolution
Analyse Crystal structure of the complex of goat lactoperoxidase with thiocyanate at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N8F
- 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
- A3F9D6
- Ligands
- HEM, NAG, BMA, CA, NO3, SCN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% helix, 9% strand | A3F9D6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 4 copies · chains A, B
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.81 | 0.84 | 77 | HEM, SCN |
| 2 | 1143 | 0.81 | 0.82 | 100 | SCN, HEM |
| 3 | 350 | 0.59 | 0.77 | 49 | empty |
| 4 | 315 | 0.59 | 0.77 | 47 | empty |
| 5 | 251 | 0.58 | 0.79 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan, 4 cofactor, 2 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 3N8F · Crystal structure of the complex of goat lactoperoxidase with thiocyanate at 3.2 A… · 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 A3F9D6
- Elsewhere: RCSB PDB 3N8F · PDBe 3N8F · UniProt A3F9D6
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