MolNFT v1 · #55010 · protein
Peroxisomal alpha-beta-hydrolase LPX1 (YOR084W) from saccharomyces cerevisiae (crystal form I)
2Y6V · Peroxisomal membrane protein LPX1: “Peroxisomal alpha-beta-hydrolase LPX1 (YOR084W) from saccharomyces cerevisiae (crystal form I)”. X-ray diffraction, 1 ligand (PO4), 14 pockets (best druggability 0.78). MolNFT v1 #55010 on…
- PDB
- 2Y6V
- Type
- protein
- Length
- 1,096 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal membrane protein LPX1
- EC
- 3.1.1.-
- UniProt
- Q12405
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal membrane protein LPX1 (EC 3.1.1.-) | protein | 356 | 40% helix, 21% strand | Q12405 |
| B | Peroxisomal membrane protein LPX1 (EC 3.1.1.-) | protein | 363 | 40% helix, 21% strand | Q12405 |
| C | Peroxisomal membrane protein LPX1 (EC 3.1.1.-) | protein | 377 | 39% helix, 18% strand | Q12405 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.78 | 0.82 | 64 | empty |
| 2 | 351 | 0.74 | 0.85 | 61 | PO4 |
| 3 | 344 | 0.72 | 0.84 | 57 | PO4 |
| 4 | 321 | 0.71 | 0.84 | 55 | PO4 |
| 5 | 413 | 0.66 | 0.79 | 45 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2960 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (oxidation, artifact).
Compared structures
- 2Y6V · Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyces cerevisiae (crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12405 · AlphaFold monomer V2.0 prediction for peroxisomal membrane protein LPX1 (Q12405) · 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 Q12405
- Elsewhere: RCSB PDB 2Y6V · PDBe 2Y6V · UniProt Q12405
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