Research workbench

Cal PDZ domain with peptide and inhibitor

Analyse Cal PDZ domain with peptide and inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IC3
Type: protein
Length: 184 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; HPV18E6 peptide
UniProt: Q9HD26
Ligands: PQR
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 3 distinct chains · 19% 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	HPV18E6 peptide	protein	6	0% helix, 33% strand	—
D	HPV18E6 peptide	protein	4	0% helix, 50% strand	—

Ligands and binding sites

PQR · 4-[methyl(nitroso)amino]benzene-1,2-diol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.31	0.74	19	empty

Interfaces

4 interfaces between chains.

A–B · 481 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 436 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 373 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 159 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5IC3 · CAL PDZ domain with peptide and inhibitor · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 5IC3 · PDBe 5IC3 · UniProt Q9HD26

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