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Crystal structure of goat lactoperoxidase complexed with a tightly bound inhibitor, 4-aminophenyl-4H-imidazole-1-yl methanone at 2.3 a resolution
Analyse Crystal structure of goat lactoperoxidase complexed with a tightly bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RKE
- 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
- A3F9D6
- Ligands
- HEM, MZZ, NAG, CA, IOD
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 8% strand | A3F9D6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- MZZ · (4-aminophenyl)-imidazol-1-yl-methanone · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 9 copies · chains A
- EDO · 1,2-ethanediol · additive · 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 | 856 | 0.80 | 0.82 | 81 | HEM, IOD, MZZ |
| 2 | 238 | 0.57 | 0.79 | 39 | empty |
| 3 | 105 | 0.44 | 0.78 | 20 | empty |
| 4 | 76 | 0.37 | 0.77 | 19 | IOD |
| 5 | 87 | 0.34 | 0.74 | 20 | empty |
Modifications
Observed in the structure: 7 disulfide, 3 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).
Compared structures
- 3RKE · Crystal Structure of goat Lactoperoxidase complexed with a tightly bound inhibitor… · 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 A3F9D6
- Elsewhere: RCSB PDB 3RKE · PDBe 3RKE · UniProt A3F9D6
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