MolNFT v1 · #104742 · protein
Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1 ångström resolution
4QJQ: “Crystal structure of goat lactoperoxidase in complex with octopamine at 2.1 ångström resolution”. X-ray diffraction, 6 ligands (HEM, OTR, NAG), 7 pockets (best druggability 0.82). MolNFT v1 #104742 on GenesisL1: 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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