Research workbench
Crystal structure of the copii coat subunit, SEC24, complexed with a peptide from the snare protein SED5 (yeast syntaxin-5)
Analyse Crystal structure of the copii coat subunit, SEC24, complexed with a peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PD0
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC24; Copii-binding peptide of the integral membrane protein…
- UniProt
- P40482, Q01590
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC24 | protein | 734 | 33% helix, 22% strand | P40482 |
| B | Copii-binding peptide of the integral membrane protein SED5 | protein | 10 | 0% helix, 10% strand | Q01590 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.85 | 0.95 | 48 | empty |
| 2 | 331 | 0.61 | 0.78 | 40 | empty |
| 3 | 281 | 0.56 | 0.77 | 31 | empty |
| 4 | 146 | 0.47 | 0.78 | 20 | empty |
| 5 | 54 | 0.45 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 667 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1PD0 · Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the… · the same entry in another collection · chain A against A, TM-score 1.00
- P40482 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24 (P40482) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q01590 · AlphaFold monomer V2.0 prediction for integral membrane protein SED5 (Q01590) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 P40482
- Every structure of UniProt Q01590
- Elsewhere: RCSB PDB 1PD0 · PDBe 1PD0 · UniProt P40482 · UniProt Q01590
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