Research workbench

Nlir - LC3B fusion protein

Analyse Nlir - LC3B fusion protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XAD
Type: protein
Length: 285 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microtubule-associated proteins 1A/1B light chain 3B; Uncharacterised protein
UniProt: Q9GZQ8, A0A129J378
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microtubule-associated proteins 1A/1B light chain 3B	protein	117	32% helix, 22% strand	Q9GZQ8
B	Microtubule-associated proteins 1A/1B light chain 3B	protein	119	34% helix, 23% strand	Q9GZQ8
C	Uncharacterised protein	protein	24	0% helix, 42% strand	A0A129J378
D	Uncharacterised protein	protein	25	0% helix, 40% strand	A0A129J378

Pockets

4 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	0.51	0.79	33	empty
2	201	0.50	0.76	31	empty
3	150	0.48	0.78	20	empty
4	83	0.33	0.74	22	empty

Interfaces

3 interfaces between chains.

A–B · 308 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 223 Å² buried · 1 hydrogen bond · protein-protein
A–C · 169 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5XAD · NLIR - LC3B fusion protein · the same entry in another collection · chain A against A, TM-score 1.00
Q9GZQ8 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9GZQ8
Every structure of UniProt A0A129J378
Elsewhere: RCSB PDB 5XAD · PDBe 5XAD · UniProt Q9GZQ8 · UniProt A0A129J378

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