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Crystal structure of sheep lactoperoxidase at 3.25 a resolution reveals the binding sites for formate
Analyse Crystal structure of sheep lactoperoxidase at 3.25 a resolution reveals the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IKC
- Type
- protein
- Length
- 1,190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Milk lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- Q9MZY2
- Ligands
- HEM, NAG, MAN, CA, CO3
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Milk lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% helix, 9% strand | Q9MZY2 |
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
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.83 | 0.85 | 90 | HEM, FMT |
| 2 | 864 | 0.81 | 0.83 | 81 | HEM, FMT |
| 3 | 591 | 0.67 | 0.77 | 68 | empty |
| 4 | 228 | 0.58 | 0.79 | 28 | empty |
| 5 | 233 | 0.55 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 461 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan, 4 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 2IKC · Crystal structure of sheep lactoperoxidase at 3.25 A resolution reveals the binding sites… · 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 Q9MZY2
- Elsewhere: RCSB PDB 2IKC · PDBe 2IKC · UniProt Q9MZY2
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