Research workbench
Crystal structure of a dimeric yak lactoperoxidase at 2.59 a resolution.
Analyse Crystal structure of a dimeric yak lactoperoxidase at 2.59 a resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LQW
- Type
- protein
- Length
- 1,190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- UniProt
- L8ICE9
- Ligands
- HEM, PEO, NAG, CA, CL
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoperoxidase | protein | 595 | 36% helix, 9% strand | L8ICE9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PEO · Hydrogen peroxide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.85 | 0.89 | 64 | HEM, PEO |
| 2 | 520 | 0.84 | 0.89 | 49 | HEM, PEO |
| 3 | 317 | 0.73 | 0.86 | 63 | empty |
| 4 | 412 | 0.72 | 0.83 | 54 | empty |
| 5 | 640 | 0.69 | 0.77 | 71 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan, 3 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 6LQW · Crystal structure of a dimeric yak lactoperoxidase at 2.59 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 6LQW · PDBe 6LQW · UniProt L8ICE9
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