Research workbench
Crystal structure of the complex of buffalo lactoperoxidase with fluoride ion at 3.5A resolution
Analyse Crystal structure of the complex of buffalo lactoperoxidase with fluoride ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z5Z
- Type
- protein
- Length
- 595 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- A5JUY8
- Ligands
- HEM, OSM, NAG, MAN, CA, IOD, F
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 9% strand | A5JUY8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- OSM · 1-(oxidosulfanyl)methanamine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 9 copies · chains A
- F · Fluoride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.81 | 0.82 | 101 | IOD, HEM, OSM |
| 2 | 258 | 0.57 | 0.78 | 31 | empty |
| 3 | 92 | 0.53 | 0.84 | 22 | empty |
| 4 | 95 | 0.34 | 0.74 | 20 | empty |
| 5 | 73 | 0.33 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 2Z5Z · Crystal structure of the complex of buffalo Lactoperoxidase with fluoride ion at 3.5A… · the same entry in another collection · chain A against A, TM-score 1.00
- A5JUY8 · AlphaFold monomer V2.0 prediction for lactoperoxidase (A5JUY8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A5JUY8
- Elsewhere: RCSB PDB 2Z5Z · PDBe 2Z5Z · UniProt A5JUY8
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