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PDLIM4 PDZ in complex with a phage-derived peptide

Analyse PDLIM4 PDZ in complex with a phage-derived peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q2O
Type: protein
Length: 531 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PDZ and lim domain protein 4
UniProt: P50479
Pockets: 2 · best druggability 0.31

Structure

x-ray diffraction · 5 distinct chains · 16% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	PDZ and lim domain protein 4	protein	92	16% helix, 37% strand	P50479
B	PDZ and lim domain protein 4	protein	89	18% helix, 38% strand	P50479
C	PDZ and lim domain protein 4	protein	88	14% helix, 39% strand	P50479
D	PDZ and lim domain protein 4	protein	84	15% helix, 36% strand	P50479
E	PDZ and lim domain protein 4	protein	86	17% helix, 38% strand	P50479

Pockets

2 pockets 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	17	empty
2	63	0.30	0.74	21	empty

Interfaces

5 interfaces between chains.

A–B · 1516 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1416 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1204 Å² buried · 22 hydrogen bonds · protein-protein
C–E · 432 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 422 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4Q2O · PDLIM4 PDZ in Complex with a Phage-Derived Peptide · the same entry in another collection · chain F against F, TM-score 1.00
P50479 · AlphaFold monomer V2.0 prediction for PDZ and lim domain protein 4 (P50479) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 P50479
Elsewhere: RCSB PDB 4Q2O · PDBe 4Q2O · UniProt P50479

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