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MLLT4/AFADIN PDZ domain in complex with the C-terminal peptide from protein E of SARS-cov-2

Analyse MLLT4/AFADIN PDZ domain in complex with the C-terminal peptide from protein E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QCR
Type: protein
Length: 183 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Afadin; Envelope small membrane protein
UniProt: P55196, P0DTC4
Ligands: SO4
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Afadin	protein	87	16% helix, 40% strand	P55196
B	Afadin	protein	86	16% helix, 41% strand	P55196
C, D	Envelope small membrane protein	protein	5	0% helix, 20% strand	P0DTC4

Ligands and binding sites

SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.60	0.82	33	empty

Interfaces

5 interfaces between chains.

A–B · 1731 Å² buried · 36 hydrogen bonds · protein-protein
A–D · 425 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 356 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 104 Å² buried · 1 hydrogen bond · protein-protein
B–D · 39 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7QCR · MLLT4/Afadin PDZ domain in complex with the C-terminal peptide from protein E of… · the same entry in another collection · chain A against A, TM-score 1.00
P55196 · AlphaFold monomer V2.0 prediction for afadin (P55196) · a predicted model of the same protein · chain B against A, TM-score 0.85

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 P55196
Every structure of UniProt P0DTC4
Elsewhere: RCSB PDB 7QCR · PDBe 7QCR · UniProt P55196 · UniProt P0DTC4

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