MolNFT v1 · #116825 · protein

Crystal structure of PLEKHM1 lir-fused human LC3A_2-121

5DPR · Pleckstrin homology domain-containing family M member 1…: “Crystal structure of PLEKHM1 lir-fused human LC3A_2-121”. X-ray diffraction, 8 pockets (best druggability 0.48). MolNFT v1 #116825 on GenesisL1: 3D structure, binding sites…

PDB: 5DPR
Type: protein
Length: 502 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pleckstrin homology domain-containing family M member 1, microtubule-associated proteins…
UniProt: Q9Y4G2, Q9H492
Pockets: 8 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Pleckstrin homology domain-containing family M member 1, microtubule-associated proteins 1A/1B light chain 3A	protein	124	30% helix, 20% strand	Q9Y4G2, Q9H492
B, C	Pleckstrin homology domain-containing family M member 1, microtubule-associated proteins 1A/1B light chain 3A	protein	127	29% helix, 20% strand	Q9Y4G2, Q9H492

Pockets

8 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	178	0.48	0.76	29	empty
2	191	0.47	0.75	36	empty
3	143	0.46	0.77	29	empty
4	164	0.45	0.75	34	empty
5	104	0.41	0.76	17	empty

Interfaces

4 interfaces between chains.

C–D · 430 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 423 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 321 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 288 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DPR · Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121 · the same entry in another collection · chain D against D, TM-score 1.00
Q9H492 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain B against A, TM-score 0.90
Q9Y4G2 · AlphaFold monomer V2.0 prediction for pleckstrin homology domain- containing family M… · a predicted model of the same protein · chain A against A, TM-score 0.37

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 Q9H492
Elsewhere: RCSB PDB 5DPR · PDBe 5DPR · UniProt Q9Y4G2 · UniProt Q9H492

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