Research workbench
Crystal structure of the complex of lactoperoxidase from bovine with 3,3-oxydipyridine at 2.31 a resolution
Analyse Crystal structure of the complex of lactoperoxidase from bovine with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NJB
- 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, 3OP, NAG, CA, IOD
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 9% strand | P80025 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 3OP · 3,3'-oxydipyridine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 11 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 1130 | 0.81 | 0.82 | 113 | HEM, IOD, 3OP |
| 2 | 327 | 0.58 | 0.77 | 44 | empty |
| 3 | 94 | 0.45 | 0.80 | 21 | empty |
| 4 | 87 | 0.37 | 0.76 | 16 | IOD |
| 5 | 62 | 0.36 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 4NJB · Crystal structure of the complex of lactoperoxidase from bovine with 3,3-oxydipyridine at… · 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 4NJB · PDBe 4NJB · UniProt P80025
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