Research workbench
Crystal structure of the complex of bovine lactoperoxidase with multiple scn and oscn ions in the distal heme cavity
Analyse Crystal structure of the complex of bovine lactoperoxidase with multiple scn… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZGS
- 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, OSM, NAG, CA, NA, IOD, SCN
- Pockets
- 7 · best druggability 0.82
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
- OSM · 1-(oxidosulfanyl)methanamine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- IOD · Iodide ion · ion · 11 copies · chains A
- SCN · Thiocyanate ion · ion · 5 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 | 1021 | 0.82 | 0.83 | 100 | HEM, SCN, IOD, OSM |
| 2 | 288 | 0.59 | 0.78 | 33 | empty |
| 3 | 112 | 0.47 | 0.79 | 20 | empty |
| 4 | 91 | 0.38 | 0.76 | 21 | IOD |
| 5 | 81 | 0.37 | 0.76 | 16 | IOD |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 1 covalent, 1 modified (disulfide, N-glycosylation, covalent ligand, phosphorylation).
Compared structures
- 5ZGS · Crystal structure of the complex of bovine lactoperoxidase with multiple SCN and OSCN… · 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 5ZGS · PDBe 5ZGS · UniProt P80025
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