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Crystal structure of yak lactoperoxidase at 1.93 a resolution.
Analyse Crystal structure of yak lactoperoxidase at 1.93 a resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L2J
- 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
- L8ICE9
- Ligands
- OSM, PEO, HEM, NAG, MAN, BMA, CA, IOD, SCN
- Pockets
- 7 · best druggability 0.80
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 | L8ICE9 |
Ligands and binding sites
- OSM · 1-(oxidosulfanyl)methanamine · ligand · 8 copies · chains A
- PEO · Hydrogen peroxide · ligand · 5 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 5 copies · chains A
- IOD · Iodide ion · ion · 26 copies · chains A
- SCN · Thiocyanate ion · ion · 12 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 | 1080 | 0.80 | 0.81 | 103 | HEM, IOD, SCN, OSM, PEO |
| 2 | 284 | 0.61 | 0.79 | 37 | CA |
| 3 | 98 | 0.47 | 0.81 | 19 | empty |
| 4 | 127 | 0.40 | 0.75 | 29 | OSM |
| 5 | 59 | 0.38 | 0.79 | 17 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 6L2J · Crystal structure of yak lactoperoxidase at 1.93 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 6L2J · PDBe 6L2J · UniProt L8ICE9
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