Research workbench
Cftr associated ligand (cal) PDZ domain bound to peptidomimetic lycalaeb
Analyse Cftr associated ligand (cal) PDZ domain bound to peptidomimetic lycalaeb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZR
- Type
- protein
- Length
- 188 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Golgi-associated PDZ and coiled-coil motif-containing protein; Lycalaeb peptide core
- UniProt
- Q9HD26
- Ligands
- VU4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Golgi-associated PDZ and coiled-coil motif-containing protein | protein | 87 | 21% helix, 43% strand | Q9HD26 |
| C | Lycalaeb peptide core | protein | 8 | 0% helix, 38% strand | — |
| D | Lycalaeb peptide core | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- VU4 · 4-(2-aminoethyl)benzoic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.36 | 0.80 | 20 | empty |
| 2 | 101 | 0.35 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 482 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 466 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 382 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 167 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7JZR · CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HD26 · AlphaFold monomer V2.0 prediction for golgi-associated PDZ and coiled-coil… · a predicted model of the same protein · chain B 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 Q9HD26
- Elsewhere: RCSB PDB 7JZR · PDBe 7JZR · UniProt Q9HD26
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