Research workbench
Crystal structure of the complex of goat lactoperoxidase with phosphate at 2.94 a resolution
Analyse Crystal structure of the complex of goat lactoperoxidase with phosphate at 2.94… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EFB
- 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, OSM, NAG, MAN, BMA, CA, PO4, CO3, CYN, SCN
- Pockets
- 13 · best druggability 0.80
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
- OSM · 1-(oxidosulfanyl)methanamine · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
- CYN · Cyanide ion · ion · chains A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.80 | 0.81 | 104 | HEM, OSM |
| 2 | 902 | 0.80 | 0.82 | 83 | HEM, CYN, SCN |
| 3 | 261 | 0.60 | 0.80 | 42 | empty |
| 4 | 236 | 0.57 | 0.78 | 34 | empty |
| 5 | 82 | 0.52 | 0.85 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2EFB · Crystal structure of the complex of goat lactoperoxidase with phosphate at 2.94 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 2EFB · PDBe 2EFB · UniProt A3F9D6
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