Research workbench
Crystal structure of the complex of bovine lactoperoxidase with mercaptoimidazole at 2.3 a resolution
Analyse Crystal structure of the complex of bovine lactoperoxidase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GH0
- 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
- P80025
- Ligands
- HEM, MZY, NAG, CA, NO3, CO3
- Pockets
- 5 · best druggability 0.80
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 | P80025 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- MZY · 1,3-dihydroimidazole-2-thione · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · chains A
- NO3 · Nitrate ion · ion · 2 copies · chains A
- CO3 · Carbonate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.80 | 0.82 | 97 | HEM, MZY |
| 2 | 282 | 0.58 | 0.77 | 33 | empty |
| 3 | 106 | 0.50 | 0.81 | 24 | empty |
| 4 | 119 | 0.42 | 0.76 | 29 | empty |
| 5 | 88 | 0.35 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 5GH0 · Crystal structure of the complex of bovine lactoperoxidase with mercaptoimidazole at 2.3… · the same entry in another collection · chain A against A, TM-score 1.00
- P80025 · AlphaFold monomer V2.0 prediction for lactoperoxidase (P80025) · 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 P80025
- Elsewhere: RCSB PDB 5GH0 · PDBe 5GH0 · UniProt P80025
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