Research workbench
Structure of peroxisomal targeting signal 2 (PTS2) of saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with PEX7P and PEX21P
Analyse Structure of peroxisomal targeting signal 2 (PTS2) of saccharomyces cerevisiae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W15
- Type
- protein
- Length
- 797 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal targeting signal 2 receptor; Peroxisomal membrane protein PEX21…
- UniProt
- P39108, P50091, P27796, P0AEX9
- Ligands
- MG, NO3
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal targeting signal 2 receptor | protein | 336 | 4% helix, 48% strand | P39108 |
| B | Peroxisomal membrane protein PEX21 | protein | 72 | 43% helix, 11% strand | P50091 |
| C | 3-ketoacyl-CoA thiolase, peroxisomal, maltose-binding periplasmic protein | protein | 389 | 48% helix, 20% strand | P27796, P0AEX9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C
- NO3 · Nitrate ion · ion · 9 copies · chains A, C, B
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 | 259 | 0.76 | 0.90 | 37 | MG |
| 2 | 315 | 0.59 | 0.77 | 38 | NO3 |
| 3 | 123 | 0.49 | 0.79 | 27 | NO3 |
| 4 | 184 | 0.45 | 0.75 | 21 | empty |
| 5 | 109 | 0.40 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1338 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1183 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 533 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3W15 · Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae… · the same entry in another collection · chain A against A, TM-score 1.00
- P39108 · AlphaFold monomer V2.0 prediction for peroxisomal targeting signal 2 receptor (P39108) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P50091 · AlphaFold monomer V2.0 prediction for peroxisomal membrane protein PEX21 (P50091) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P27796 · AlphaFold monomer V2.0 prediction for 3-ketoacyl-CoA thiolase, peroxisomal (P27796) · a predicted model of the same protein · chain C against A, TM-score 0.27
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 P39108
- Every structure of UniProt P50091
- Every structure of UniProt P27796
- Every structure of UniProt P0AEX9
- Elsewhere: RCSB PDB 3W15 · PDBe 3W15 · UniProt P39108 · UniProt P50091 · UniProt P27796 · UniProt P0AEX9
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