Research workbench
Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.
Analyse Structure of bovine lactoperoxidase with multiple iodide ions in the distaline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M7E
- 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, IOD, SCN, CL
- Pockets
- 7 · best druggability 0.83
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
- 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
- IOD · Iodide ion · ion · 16 copies · chains A
- SCN · Thiocyanate ion · ion · 4 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.83 | 0.83 | 97 | HEM, IOD, SCN |
| 2 | 118 | 0.46 | 0.79 | 25 | empty |
| 3 | 125 | 0.42 | 0.76 | 23 | empty |
| 4 | 80 | 0.35 | 0.75 | 17 | IOD |
| 5 | 78 | 0.35 | 0.76 | 19 | SCN |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 6M7E · Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme… · 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 6M7E · PDBe 6M7E · UniProt P80025
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