MolNFT v1 · #47399 · protein
Structure of the human pancreatic lipase-related protein 2
2OXE: “Structure of the human pancreatic lipase-related protein 2”. X-ray diffraction, 4 ligands (MAN, NAG, CA), 4 pockets (best druggability 0.45). MolNFT v1 #47399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2OXE
- Type
- protein
- Length
- 866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic lipase-related protein 2
- EC
- 3.1.1.3
- UniProt
- P54317
- Ligands
- MAN, NAG, CA, CL
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pancreatic lipase-related protein 2 (EC 3.1.1.3) | protein | 435 | 22% helix, 31% strand | P54317 |
| B | Pancreatic lipase-related protein 2 (EC 3.1.1.3) | protein | 431 | 22% helix, 31% strand | P54317 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.45 | 0.78 | 19 | empty |
| 2 | 88 | 0.38 | 0.76 | 17 | empty |
| 3 | 116 | 0.37 | 0.74 | 23 | empty |
| 4 | 96 | 0.34 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 356 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2OXE · Structure of the Human Pancreatic Lipase-related Protein 2 · the same entry in another collection · chain A against A, TM-score 1.00
- P54317 · AlphaFold monomer V2.0 prediction for pancreatic lipase-related protein 2 (P54317) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P54317
- Elsewhere: RCSB PDB 2OXE · PDBe 2OXE · UniProt P54317
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