Research workbench
Cftr associated ligand (cal) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide (rlqrrretqv)
Analyse Cftr associated ligand (cal) PDZ domain bound to HPV18 E6 oncoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JOR
- Type
- protein
- Length
- 189 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; Protein E6
- UniProt
- Q9HD26, P06463
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Golgi-associated PDZ and coiled-coil motif-containing protein | protein | 87 | 21% helix, 44% strand | Q9HD26 |
| C | Protein E6 | protein | 10 | 0% helix, 30% strand | P06463 |
| D | Protein E6 | protein | 5 | 0% helix, 60% strand | P06463 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 137 | 0.43 | 0.76 | 25 | empty |
| 2 | 55 | 0.34 | 0.79 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 493 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 392 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4JOR · CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide… · 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 A 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
- Every structure of UniProt P06463
- Elsewhere: RCSB PDB 4JOR · PDBe 4JOR · UniProt Q9HD26 · UniProt P06463
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.