Research workbench
Cftr associated ligand (cal) PDZ domain bound to peptide ICAL36-trl (ansrwpttrl)
Analyse Cftr associated ligand (cal) PDZ domain bound to peptide ICAL36-trl (ansrwpttrl) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K76
- Type
- protein
- Length
- 378 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Golgi-associated PDZ and coiled-coil motif-containing protein; ICAL36-trl peptide
- UniProt
- Q9HD26
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Golgi-associated PDZ and coiled-coil motif-containing protein | protein | 87 | 21% helix, 43% strand | Q9HD26 |
| E | ICAL36-trl peptide | protein | 8 | 0% helix, 38% strand | — |
| F | ICAL36-trl peptide | protein | 9 | 0% helix, 33% strand | — |
| G | ICAL36-trl peptide | protein | 7 | 0% helix, 29% strand | — |
| H | ICAL36-trl peptide | protein | 6 | 0% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.66 | 0.77 | 65 | GOL |
| 2 | 94 | 0.36 | 0.75 | 18 | empty |
| 3 | 55 | 0.34 | 0.78 | 15 | empty |
Interfaces
11 interfaces between chains.
- D–H · 542 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 538 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 537 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 510 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4K76 · CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-TRL (ANSRWPTTRL) · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.98
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 4K76 · PDBe 4K76 · UniProt Q9HD26
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