Research workbench
Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 a resolution
Analyse Crystal structure of the complex of dimeric goat lactoperoxidase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NIU
- 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, PO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 36% helix, 10% 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 · 14 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.80 | 0.82 | 79 | HEM, PEG |
| 2 | 802 | 0.80 | 0.83 | 80 | HEM, PEG |
| 3 | 239 | 0.60 | 0.80 | 38 | empty |
| 4 | 207 | 0.53 | 0.78 | 33 | empty |
| 5 | 195 | 0.49 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 101 Ų buried · 3 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
- 3NIU · Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol… · 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 3NIU · PDBe 3NIU · UniProt A3F9D6
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