Research workbench
Crystal structure of yak lactoperoxidase with partially coordinated na ion in the distal heme cavity
Analyse Crystal structure of yak lactoperoxidase with partially coordinated na ion in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C75
- 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, K, ZN, NA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase | protein | 595 | 37% helix, 8% strand | L8ICE9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- K · Potassium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.82 | 0.84 | 89 | HEM, NA |
| 2 | 250 | 0.51 | 0.75 | 29 | empty |
| 3 | 124 | 0.45 | 0.77 | 31 | empty |
| 4 | 93 | 0.44 | 0.79 | 19 | empty |
| 5 | 67 | 0.31 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 7C75 · Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal… · 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 7C75 · PDBe 7C75 · UniProt L8ICE9
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