Research workbench
Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in MGCL2 at 2.70 a resolution
Analyse Crystal structure of yak lactoperoxidase using data obtained from crystals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C73
- Type
- protein
- Length
- 595 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- UniProt
- L8ICE9
- Ligands
- HEM, NAG, CA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase | protein | 595 | 38% helix, 10% strand | L8ICE9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 2 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 | 834 | 0.81 | 0.84 | 79 | HEM |
| 2 | 142 | 0.51 | 0.80 | 29 | empty |
| 3 | 111 | 0.44 | 0.78 | 22 | empty |
| 4 | 79 | 0.35 | 0.75 | 16 | empty |
| 5 | 63 | 0.34 | 0.77 | 18 | empty |
Modifications
Observed in the structure: 7 disulfide, 3 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 7C73 · Crystal structure of yak lactoperoxidase using data obtained from crystals soaked in… · 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 7C73 · PDBe 7C73 · UniProt L8ICE9
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