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Structure of peroxisomal targeting signal 1 (PTS1) binding domain of trypanosoma brucei peroxin 5 (TBPEX5)COMPLEXED to T. brucei phosphoglucoisomerase (pgi) PTS1 peptide
Analyse Structure of peroxisomal targeting signal 1 (PTS1) binding domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CV0
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome targeting signal 1 receptor PEX5; T. brucei pgi PTS1 peptide ac-fnelshl
- UniProt
- Q9U7C3, P13377
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome targeting signal 1 receptor PEX5 | protein | 300 | 69% helix, 0% strand | Q9U7C3 |
| B | T. brucei pgi PTS1 peptide ac-fnelshl | protein | 6 | 0% helix, 0% strand | P13377 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.57 | 0.79 | 35 | EDO |
| 2 | 232 | 0.53 | 0.77 | 41 | empty |
| 3 | 51 | 0.40 | 0.82 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 581 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3CV0 · Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei… · the same entry in another collection · chain A against A, TM-score 1.00
- P13377 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate isomerase, glycosomal (P13377) · a predicted model of the same protein · chain B against A, TM-score 0.63
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 Q9U7C3
- Every structure of UniProt P13377
- Elsewhere: RCSB PDB 3CV0 · PDBe 3CV0 · UniProt Q9U7C3 · UniProt P13377
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