Research workbench
Crystal structure of the human COPII-coat protein Sec24c
Analyse Crystal structure of the human COPII-coat protein Sec24c in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EH2
- Type
- protein
- Length
- 2,236 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens
- Molecule
- Protein transport protein Sec24C
- UniProt
- P53992
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.35 · 3 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein Sec24C | protein | 758 | 34% helix, 21% strand | P53992 |
| B | Protein transport protein Sec24C | protein | 739 | 31% helix, 21% strand | P53992 |
| C | Protein transport protein Sec24C | protein | 739 | 31% helix, 21% strand | P53992 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.83 | 0.85 | 87 | empty |
| 2 | 676 | 0.76 | 0.81 | 56 | empty |
| 3 | 571 | 0.76 | 0.83 | 63 | empty |
| 4 | 104 | 0.75 | 0.96 | 23 | empty |
| 5 | 538 | 0.75 | 0.82 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1262 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1040 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 76 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3EH2 · Crystal structure of the human copii-coat protein SEC24C · the same entry in another collection · chain A against A, TM-score 1.00
- P53992 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24C (P53992) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P53992
- Elsewhere: RCSB PDB 3EH2 · PDBe 3EH2 · UniProt P53992
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