Research workbench
Crystal structure of bovine lactoperoxidase with substrates thiocynate and iodide bound at the distal heme side at 1.99 a resolution.
Analyse Crystal structure of bovine lactoperoxidase with substrates thiocynate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCO
- 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
- OSM, HEM, NAG, CA, IOD, SCN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% helix, 10% strand | P80025 |
Ligands and binding sites
- OSM · 1-(oxidosulfanyl)methanamine · ligand · 3 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 16 copies · chains A
- SCN · Thiocyanate ion · ion · 7 copies · chains A
- EDO · 1,2-ethanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.83 | 0.84 | 99 | HEM, IOD, EDO, SCN, OSM |
| 2 | 182 | 0.48 | 0.76 | 25 | empty |
| 3 | 122 | 0.47 | 0.79 | 23 | empty |
| 4 | 147 | 0.45 | 0.76 | 38 | empty |
| 5 | 71 | 0.36 | 0.77 | 18 | IOD, SCN |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 6LCO · Crystal structure of bovine lactoperoxidase with substrates thiocynate and iodide bound… · 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 6LCO · PDBe 6LCO · UniProt P80025
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