Research workbench
Crystal structure of the complex of buffalo lactoperoxidase with salicylhydroxamic acid at 2.48 a resolution
Analyse Crystal structure of the complex of buffalo lactoperoxidase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FNL
- 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
- Ligands
- HEM, SHA, NAG, MAN, CA, IOD, SCN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 10% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- SHA · Salicylhydroxamic acid · 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 · 8 copies · chains A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.81 | 0.83 | 80 | HEM, SHA |
| 2 | 352 | 0.60 | 0.77 | 51 | empty |
| 3 | 98 | 0.50 | 0.82 | 23 | empty |
| 4 | 53 | 0.35 | 0.78 | 12 | empty |
| 5 | 85 | 0.33 | 0.74 | 20 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 3FNL · Crystal Structure of the Complex of Buffalo Lactoperoxidase with Salicylhydroxamic Acid… · 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
- Elsewhere: RCSB PDB 3FNL · PDBe 3FNL
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