Research workbench

Cal PDZ mutant C319A with a peptide

Analyse Cal PDZ mutant C319A with a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K4F
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, P06463
Pockets: 1 · best druggability 0.26

Structure

x-ray diffraction · 3 distinct chains · 19% 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, 41% strand	Q9HD26
C	HPV18E6 peptide	protein	6	0% helix, 50% strand	P06463
D	HPV18E6 peptide	protein	4	0% helix, 50% strand	P06463

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	50	0.26	0.74	14	empty

Interfaces

4 interfaces between chains.

A–C · 428 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 393 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 351 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 163 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5K4F · CAL PDZ mutant C319A with a 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 5K4F · PDBe 5K4F · UniProt Q9HD26 · UniProt P06463

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