Research workbench
Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1 ångström resolution
Analyse Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QJQ
- 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
- A3F9D6
- Ligands
- HEM, OTR, NAG, CA, IOD, SCN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 39% helix, 9% strand | A3F9D6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- OTR · 4-(2R-amino-1-hydroxyethyl)phenol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 13 copies · chains A
- SCN · Thiocyanate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.82 | 0.84 | 78 | HEM, IOD, SCN, OTR |
| 2 | 317 | 0.59 | 0.77 | 43 | EDO |
| 3 | 123 | 0.47 | 0.79 | 21 | empty |
| 4 | 87 | 0.36 | 0.75 | 16 | IOD |
| 5 | 52 | 0.36 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 4QJQ · Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1 Angstrom… · 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 4QJQ · PDBe 4QJQ · UniProt A3F9D6
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