MolNFT v1 · #35638 · protein
Crystal structure of goat lactoperoxidase complexed with formate anion at 3.3 a resolution
2EHA: “Crystal structure of goat lactoperoxidase complexed with formate anion at 3.3 a resolution”. X-ray diffraction, 8 ligands (HEM, OSM, NAG), 15 pockets (best druggability 0.82). MolNFT v1 #35638 on GenesisL1: 3D structure, binding…
- PDB
- 2EHA
- Type
- protein
- Length
- 1,190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- A3F9D6
- Ligands
- HEM, OSM, NAG, MAN, BMA, CA, CO3, SCN
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactoperoxidase (EC 1.11.1.7) | protein | 595 | 38% helix, 9% strand | A3F9D6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OSM · 1-(oxidosulfanyl)methanamine · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · chains A
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.82 | 0.85 | 91 | SCN, HEM |
| 2 | 910 | 0.82 | 0.84 | 94 | HEM, OSM |
| 3 | 343 | 0.65 | 0.80 | 48 | empty |
| 4 | 190 | 0.53 | 0.78 | 31 | empty |
| 5 | 157 | 0.47 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 417 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2EHA · Crystal structure of goat lactoperoxidase complexed with formate anion at 3.3 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 A3F9D6
- Elsewhere: RCSB PDB 2EHA · PDBe 2EHA · UniProt A3F9D6
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