MolNFT v1 · #155141 · protein
Crystal structure of yak lactoperoxidase at 2.27 a resolution
6KY7: “Crystal structure of yak lactoperoxidase at 2.27 a resolution”. X-ray diffraction, 7 ligands (OSM, HEM, PEO), 7 pockets (best druggability 0.80). MolNFT v1 #155141 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KY7
- Type
- protein
- Length
- 595 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- UniProt
- L8ICE9
- Ligands
- OSM, HEM, PEO, NAG, CA, IOD, SCN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase | protein | 595 | 36% helix, 9% strand | L8ICE9 |
Ligands and binding sites
- OSM · 1-(oxidosulfanyl)methanamine · ligand · 4 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PEO · Hydrogen peroxide · 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 · 4 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 | 1197 | 0.80 | 0.81 | 108 | HEM, IOD, OSM, SCN, PEO |
| 2 | 237 | 0.52 | 0.76 | 31 | empty |
| 3 | 101 | 0.46 | 0.80 | 20 | empty |
| 4 | 79 | 0.41 | 0.79 | 17 | empty |
| 5 | 94 | 0.39 | 0.76 | 17 | IOD |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 6KY7 · Crystal structure of yak lactoperoxidase at 2.27 A resolution · 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 L8ICE9
- Elsewhere: RCSB PDB 6KY7 · PDBe 6KY7 · UniProt L8ICE9
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