MolNFT v1 · #116827 · protein

Crystal structure of PLEKHM1 lir-fused human GABARAPL1_2-117

5DPT · Pleckstrin homology domain-containing family M member 1…: “Crystal structure of PLEKHM1 lir-fused human GABARAPL1_2-117”. X-ray diffraction, 5 pockets (best druggability 0.53). MolNFT v1 #116827 on GenesisL1: 3D structure, binding…

PDB: 5DPT
Type: protein
Length: 245 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid…
UniProt: Q9Y4G2, Q9H0R8
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein-like 1,GAMMA- aminobutyric acid receptor-associated protein-like 1	protein	122	31% helix, 24% strand	Q9Y4G2, Q9H0R8
B	Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein-like 1,GAMMA- aminobutyric acid receptor-associated protein-like 1	protein	123	31% helix, 21% strand	Q9Y4G2, Q9H0R8

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B

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

Pockets

5 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	168	0.53	0.79	22	empty
2	149	0.46	0.77	19	empty
3	84	0.42	0.79	18	empty
4	64	0.33	0.76	18	empty
5	50	0.25	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 761 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5DPT · Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117 · the same entry in another collection · chain A against A, TM-score 1.00
Q9H0R8 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor-associated… · a predicted model of the same protein · chain A against A, TM-score 0.92
Q9Y4G2 · AlphaFold monomer V2.0 prediction for pleckstrin homology domain- containing family M… · a predicted model of the same protein · chain B against A, TM-score 0.35

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 Q9Y4G2
Every structure of UniProt Q9H0R8
Elsewhere: RCSB PDB 5DPT · PDBe 5DPT · UniProt Q9Y4G2 · UniProt Q9H0R8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.