MolNFT v1 · #152997 · protein

Crystal structure of full length human LC3B delta G120 mutant (2_125)

6J04 · Microtubule-associated proteins 1A/1B light chain 3B: “Crystal structure of full length human LC3B delta G120 mutant (2_125)”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.64). MolNFT v1 #152997 on GenesisL1: 3D…

PDB: 6J04
Type: protein
Length: 474 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microtubule-associated proteins 1A/1B light chain 3B
UniProt: Q9GZQ8
Ligands: SO4
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microtubule-associated proteins 1A/1B light chain 3B	protein	117	35% helix, 24% strand	Q9GZQ8
B	Microtubule-associated proteins 1A/1B light chain 3B	protein	116	35% helix, 24% strand	Q9GZQ8
C	Microtubule-associated proteins 1A/1B light chain 3B	protein	120	34% helix, 22% strand	Q9GZQ8
D	Microtubule-associated proteins 1A/1B light chain 3B	protein	121	36% helix, 21% strand	Q9GZQ8

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B, D

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	691	0.64	0.74	73	empty
2	168	0.44	0.74	31	empty
3	116	0.39	0.75	22	empty
4	113	0.36	0.73	22	empty
5	88	0.35	0.75	16	empty

Interfaces

6 interfaces between chains.

A–B · 370 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 192 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 135 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 124 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 78 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6J04 · Crystal structure of full length human LC3B delta G120 mutant (2_125) · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.97

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
Elsewhere: RCSB PDB 6J04 · PDBe 6J04 · UniProt Q9GZQ8

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