Research workbench
First structural evidence of substrate specificity in mammalian peroxidases: crystal structures of substrate complexes with lactoperoxidases from two different species
Analyse First structural evidence of substrate specificity in mammalian peroxidases… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ERH
- 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
- A5JUY8
- Ligands
- HEM, NAG, MAN, BMA, CA, IOD, SCN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% helix, 9% 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
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 | 710 | 0.81 | 0.85 | 64 | HEM, SCN |
| 2 | 204 | 0.55 | 0.79 | 31 | empty |
| 3 | 105 | 0.49 | 0.81 | 15 | empty |
| 4 | 97 | 0.48 | 0.81 | 24 | empty |
| 5 | 160 | 0.45 | 0.75 | 34 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 3ERH · First structural evidence of substrate specificity in mammalian peroxidases: Crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- A5JUY8 · AlphaFold monomer V2.0 prediction for lactoperoxidase (A5JUY8) · 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 A5JUY8
- Elsewhere: RCSB PDB 3ERH · PDBe 3ERH · UniProt A5JUY8
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