MolNFT v1 · #183533 · protein

PALS1 PDZ1 domain with SARS-cov-2_E pbm complex

7NTK · Maguk P55 subfamily member 5: “PALS1 PDZ1 domain with SARS-cov-2_E pbm complex”. X-ray diffraction, 2 pockets (best druggability 0.64). MolNFT v1 #183533 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7NTK
Type: protein
Length: 370 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maguk P55 subfamily member 5; Envelope small membrane protein
UniProt: Q8N3R9, P0DTC4
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F	Maguk P55 subfamily member 5	protein	86	20% helix, 42% strand	Q8N3R9
B	Maguk P55 subfamily member 5	protein	85	20% helix, 41% strand	Q8N3R9
C, E, G	Envelope small membrane protein	protein	7	0% helix, 29% strand	P0DTC4
H	Envelope small membrane protein	protein	6	0% helix, 33% strand	P0DTC4

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, E, F
FLC · Citrate anion · additive · chains B, D

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.64	0.76	53	empty
2	51	0.32	0.77	11	EDO

Interfaces

12 interfaces between chains.

A–C · 485 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 482 Å² buried · 11 hydrogen bonds · protein-protein
B–G · 479 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 476 Å² buried · 12 hydrogen bonds · protein-protein
F–H · 459 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7NTK · PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex · the same entry in another collection · chain H against H, TM-score 1.00
Q8N3R9 · AlphaFold monomer V2.0 prediction for maguk P55 subfamily member 5 (Q8N3R9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q8N3R9
Every structure of UniProt P0DTC4
Elsewhere: RCSB PDB 7NTK · PDBe 7NTK · UniProt Q8N3R9 · UniProt P0DTC4

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