Research workbench
Crystal structure of the CBLN1 C1Q domain trimer in complex with the amino-terminal domain (atd) of iglur delta-2 (GLUD2)
Analyse Crystal structure of the CBLN1 C1Q domain trimer in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KCA
- Type
- protein
- Length
- 807 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cerebellin-1,CEREBELLIN-1,CEREBELLIN-1,GLUTAMATE receptor ionotropic, delta-2
- UniProt
- P23435, O43424
- Ligands
- CA
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cerebellin-1,CEREBELLIN-1,CEREBELLIN-1,GLUTAMATE receptor ionotropic, delta-2 | protein | 807 | 21% helix, 39% strand | P23435, O43424 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.85 | 0.95 | 73 | empty |
| 2 | 347 | 0.70 | 0.83 | 36 | empty |
| 3 | 253 | 0.55 | 0.77 | 37 | empty |
| 4 | 216 | 0.55 | 0.78 | 36 | empty |
| 5 | 198 | 0.53 | 0.77 | 23 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5KCA · Crystal structure of the Cbln1 C1q domain trimer in complex with the amino-terminal… · the same entry in another collection · chain A against A, TM-score 1.00
- O43424 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, delta-2 (O43424) · a predicted model of the same protein · chain A against A, TM-score 0.51
- P23435 · AlphaFold monomer V2.0 prediction for cerebellin-1 (P23435) · a predicted model of the same protein · chain A against A, TM-score 0.18
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 P23435
- Every structure of UniProt O43424
- Elsewhere: RCSB PDB 5KCA · PDBe 5KCA · UniProt P23435 · UniProt O43424
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.