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Structure of erbin PDZ derivative E-14 with a high-affinity peptide

Analyse Structure of erbin PDZ derivative E-14 with a high-affinity peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q0M
Type: protein
Length: 201 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Erbin; Peptide
UniProt: Q96RT1
Ligands: NA, CL
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Erbin	protein	93	11% helix, 39% strand	Q96RT1
B	Erbin	protein	94	11% helix, 38% strand	Q96RT1
C, D	Peptide	protein	7	0% helix, 14% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains B
CL · Chloride ion · ion · 2 copies · chains B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
ACT · Acetate ion · additive · 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	136	0.49	0.79	20	EDO, NA

Interfaces

4 interfaces between chains.

B–D · 641 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 598 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 542 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6Q0M · Structure of Erbin PDZ derivative E-14 with a high-affinity peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q96RT1 · AlphaFold monomer V2.0 prediction for erbin (Q96RT1) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q96RT1
Elsewhere: RCSB PDB 6Q0M · PDBe 6Q0M · UniProt Q96RT1

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