Research workbench
Structure of CDK5R1-bound FEM1C
Analyse Structure of CDK5R1-bound FEM1C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDP
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens
- Molecule
- Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1
- UniProt
- Q96JP0, Q15078
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 56% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1 | protein | 387 | 57% helix, 3% strand | Q96JP0, Q15078 |
| B | Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1 | protein | 368 | 54% helix, 4% strand | Q96JP0, Q15078 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.61 | 0.78 | 33 | empty |
| 2 | 219 | 0.55 | 0.78 | 35 | empty |
| 3 | 80 | 0.54 | 0.85 | 21 | empty |
| 4 | 294 | 0.48 | 0.72 | 34 | empty |
| 5 | 156 | 0.45 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6LDP · Structure of CDK5R1-bound FEM1C · the same entry in another collection · chain A against A, TM-score 1.00
- Q96JP0 · AlphaFold monomer V2.0 prediction for protein fem-1 homolog C (Q96JP0) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q15078 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 5 activator 1 (Q15078) · a predicted model of the same protein · chain B against A, TM-score 0.22
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 Q96JP0
- Every structure of UniProt Q15078
- Elsewhere: RCSB PDB 6LDP · PDBe 6LDP · UniProt Q96JP0 · UniProt Q15078
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