MolNFT v1 · #18066 · protein
Crystal structure of the copii coat subunit, SEC24, complexed with a peptide containing the dxe cargo sorting signal of yeast SYS1 protein
1PD1 · Protein transport protein SEC24: “Crystal structure of the copii coat subunit, SEC24, complexed with a peptide containing the dxe cargo sorting…”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 1PD1
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC24; Dxe cargo sorting signal peptide of yeast SYS1 protein
- UniProt
- P40482
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC24 | protein | 735 | 33% helix, 23% strand | P40482 |
| B | Dxe cargo sorting signal peptide of yeast SYS1 protein | protein | 9 | 0% helix, 0% strand | — |
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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.81 | 0.89 | 51 | empty |
| 2 | 356 | 0.61 | 0.78 | 44 | empty |
| 3 | 260 | 0.55 | 0.77 | 29 | empty |
| 4 | 246 | 0.51 | 0.75 | 34 | empty |
| 5 | 97 | 0.44 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1PD1 · Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide containing… · 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
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
- Elsewhere: RCSB PDB 1PD1 · PDBe 1PD1 · UniProt P40482
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