Research workbench
Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.20 a resolution
Analyse Crystal structure of potassium induced heme modification in yak lactoperoxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DMR
- 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
- HEM, NAG, ZN, CA, K, CL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 37% 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 · 5 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.82 | 0.83 | 84 | HEM, K |
| 2 | 84 | 0.47 | 0.81 | 20 | empty |
| 3 | 110 | 0.41 | 0.76 | 27 | empty |
| 4 | 76 | 0.39 | 0.78 | 16 | empty |
| 5 | 53 | 0.36 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
- 7DMR · Crystal structure of potassium induced heme modification in yak lactoperoxidase at 2.20 A… · 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 7DMR · PDBe 7DMR · UniProt L8ICE9
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