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Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: binding studies and structure determination
Analyse Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HPW
- Type
- protein
- Length
- 2,380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- UniProt
- A3F9D6
- Ligands
- 3CJ, HEM, NAG, CA, NO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lactoperoxidase | protein | 595 | 36% helix, 9% strand | A3F9D6 |
Ligands and binding sites
- 3CJ · 6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one · ligand · 4 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, D, B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.84 | 0.85 | 94 | empty |
| 2 | 1022 | 0.84 | 0.85 | 87 | empty |
| 3 | 479 | 0.83 | 0.90 | 48 | 3CJ, HEM |
| 4 | 839 | 0.81 | 0.83 | 77 | HEM, 3CJ |
| 5 | 900 | 0.81 | 0.83 | 84 | 3CJ, HEM |
Interfaces
5 interfaces between chains.
- A–D · 759 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 718 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 437 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 377 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 11 glycan, 8 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 5HPW · Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies… · 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 5HPW · PDBe 5HPW · UniProt A3F9D6
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