Research workbench
Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: structure of the complex of lactoperoxidase with methimazole at 1.97 ångström resolution
Analyse Two way mode of binding of antithyroid drug methimazole to mammalian heme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FF1
- Type
- protein
- Length
- 1,190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- UniProt
- A3F9D6
- Ligands
- MMZ, HEM, NAG, CA, NO3
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoperoxidase | protein | 595 | 38% helix, 9% strand | A3F9D6 |
Ligands and binding sites
- MMZ · 1-methyl-1,3-dihydro-2H-imidazole-2-thione · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.83 | 0.86 | 73 | MMZ, HEM |
| 2 | 1005 | 0.83 | 0.84 | 87 | MMZ, HEM, GOL |
| 3 | 1116 | 0.82 | 0.83 | 124 | GOL |
| 4 | 92 | 0.44 | 0.79 | 20 | empty |
| 5 | 83 | 0.43 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan, 4 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 5FF1 · Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases… · 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 5FF1 · PDBe 5FF1 · UniProt A3F9D6
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