MolNFT v1 · #38012 · protein
Crystal structure of buffalo lactoperoxidase at 2.75A resolution
2GJM: “Crystal structure of buffalo lactoperoxidase at 2.75A resolution”. X-ray diffraction, 8 ligands (HEM, NAG, MAN), 7 pockets (best druggability 0.81). MolNFT v1 #38012 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GJM
- Type
- protein
- Length
- 583 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoperoxidase
- EC
- 1.11.1.7
- UniProt
- A5JUY8
- Ligands
- HEM, NAG, MAN, BMA, CA, IOD, SCN, CO3
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactoperoxidase (EC 1.11.1.7) | protein | 583 | 38% helix, 10% strand | A5JUY8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 8 copies · chains A
- SCN · Thiocyanate ion · ion · chains A
- CO3 · Carbonate 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 | 1021 | 0.81 | 0.82 | 81 | SCN, IOD, HEM |
| 2 | 94 | 0.48 | 0.81 | 22 | empty |
| 3 | 101 | 0.41 | 0.77 | 23 | empty |
| 4 | 101 | 0.40 | 0.77 | 24 | empty |
| 5 | 57 | 0.37 | 0.79 | 23 | empty |
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 cofactor (disulfide, N-glycosylation, heme attachment).
Compared structures
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 A5JUY8
- Elsewhere: RCSB PDB 2GJM · PDBe 2GJM · UniProt A5JUY8
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