6TBE: LC3A

LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate. Determined by X-ray diffraction at 1.67 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 1.67 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,142
Mol. weight: 14.77 kDa
Ligands: NOV
Released: 18 Nov 2020

Explore 6TBE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TBE contains 6 α-helices and 7 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-30	14
β-strand	34-41	8	1
α-helix	49-51	3
β-strand	55-59	5	1
β-strand	63	1	2
α-helix	64-75	12
β-strand	84-87	4	1
β-strand	90-91	2	1
β-strand	98	1	2
α-helix	99-106	8
α-helix	112	1
β-strand	113-118	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Microtubule-associated proteins 1A/1B light chain 3A	A	protein	119	Homo sapiens	Q9H492 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6TBE_1 Microtubule-associated proteins 1A/1B light chain 3A (chains A)
GAMDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNM
SELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETF

Ligands and cofactors

ID	Name	Formula	Copies
NOV	Novobiocin	C31 H36 N2 O11	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Demonstrating Ligandability of the LC3A and LC3B Adapter Interface. Hartmann, M., Huber, J., Kramer, J.S. et al. J Med Chem (2021) 64:3720-3746. DOI 10.1021/acs.jmedchem.0c01564 · PubMed

Other PDB entries of the same protein (UniProt Q9H492 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RA0 1.36 Å, LC3A in complex with Fragment 2-10
7R9Z 1.72 Å, LC3A in complex with Fragment 2-3
7R9W 1.75 Å, LC3A in complex with Fragment 1-1
3WAN 1.77 Å, Crystal structure of Atg13 LIR-fused human LC3A_2-121
4ZDV 1.8 Å, Crystal structure of LC3 in complex with FAM134B LIR
8T36 1.85 Å, Crystal structure of K49 acetylated LC3A in complex with the LIR of TP53INP2/DOR
8T35 1.9 Å, Crystal structure of K51 acetylated LC3A in complex with the LIR of TP53INP2/DOR
3WAL 2.0 Å, Crystal structure of human LC3A_2-121
8T2L 2.24 Å, Crystal structure of LC3A in complex with the LIR of NSs4
5CX3 2.3 Å, Crystal structure of FYCO1 LIR in complex with LC3A
8T4T 2.36 Å, Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR
5DPR 2.5 Å, Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121

Browse structure collections

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