Research workbench
Structure of the complex of sheep lactoperoxidase with hypoiodite at 2.70 a resolution
Analyse Structure of the complex of sheep lactoperoxidase with hypoiodite at 2.70 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VE3
- 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
- Q9MZY2
- Ligands
- 61D, HEM, NAG, CA, IOD, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 39% helix, 9% strand | Q9MZY2 |
Ligands and binding sites
- 61D · hypoiodous acid · ligand · 11 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 6 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.80 | 0.82 | 73 | HEM, 61D |
| 2 | 401 | 0.58 | 0.75 | 50 | empty |
| 3 | 54 | 0.45 | 0.84 | 23 | empty |
| 4 | 126 | 0.43 | 0.76 | 16 | 61D |
| 5 | 88 | 0.41 | 0.78 | 21 | empty |
Modifications
Observed in the structure: 7 disulfide, 2 cofactor, 2 glycan (disulfide, heme attachment, N-glycosylation).
Compared structures
- 7VE3 · Structure of the complex of sheep lactoperoxidase with hypoiodite at 2.70 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 Q9MZY2
- Elsewhere: RCSB PDB 7VE3 · PDBe 7VE3 · UniProt Q9MZY2
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