MolNFT v1 · #63469 · protein
Crystal structure of lactoperoxidase complex with cyanide
3FAQ: “Crystal structure of lactoperoxidase complex with cyanide”. X-ray diffraction, 8 ligands (HEM, NAG, MAN), 8 pockets (best druggability 0.81). MolNFT v1 #63469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FAQ
- Type
- protein
- Length
- 595 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- UniProt
- A5JUY8
- Ligands
- HEM, NAG, MAN, BMA, CA, IOD, SCN, CYN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase | protein | 595 | 37% helix, 10% strand | A5JUY8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 7 copies · chains A
- SCN · Thiocyanate ion · ion · 2 copies · chains A
- CYN · Cyanide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.81 | 0.82 | 86 | HEM, SCN, CYN |
| 2 | 182 | 0.52 | 0.78 | 28 | empty |
| 3 | 103 | 0.50 | 0.82 | 22 | empty |
| 4 | 160 | 0.49 | 0.78 | 32 | empty |
| 5 | 64 | 0.37 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
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 3FAQ · PDBe 3FAQ · UniProt A5JUY8
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