9BD2: MAGE-A3 MHD crystal soaked with KL861

MAGE-A3 MHD crystal soaked with KL861. Determined by X-ray diffraction at 2.24 Å resolution. Released 18 Sept 2024.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,066
Mol. weight: 71.56 kDa
Ligands: A1AL3
Released: 18 Sept 2024

Explore 9BD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BD2 contains 44 α-helices and 18 β-strands across 3 chains. 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: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
β-strand	29-30	2	1
α-helix	31-35	5
α-helix	40-45	6
α-helix	46-56	11
α-helix	57-61	5
β-strand	63-69	7	1
β-strand	74-79	6	1
α-helix	80-82	3
α-helix	98-111	14
β-strand	114-116	3	2
α-helix	117-124	8
α-helix	128-130	3
α-helix	141-151	11
β-strand	155-159	5	2
α-helix	160	1
β-strand	168-172	5	2
α-helix	174-179	6
α-helix	182-193	12
α-helix	199-201	3

Chain B: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
β-strand	29-30	2	3
α-helix	31-34	4
α-helix	35-39	5
α-helix	40-45	6
α-helix	46-56	11
α-helix	57-61	5
β-strand	63-69	7	3
β-strand	74-79	6	3
α-helix	80-82	3
α-helix	98-111	14
β-strand	114-116	3	4
α-helix	117-125	9
α-helix	128-130	3
α-helix	141-151	11
β-strand	155-159	5	4
α-helix	160	1
β-strand	168-172	5	4
α-helix	174-179	6
α-helix	182-193	12
α-helix	201-203	3
α-helix	204-206	3

Chain C: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-24	23
β-strand	29-30	2	5
α-helix	31-35	5
α-helix	40-45	6
α-helix	46-56	11
α-helix	57-61	5
β-strand	63-69	7	5
β-strand	74-79	6	5
α-helix	80-82	3
α-helix	98-111	14
β-strand	114-116	3	6
α-helix	117-125	9
α-helix	128-130	3
α-helix	141-151	11
β-strand	155-159	5	6
α-helix	160	1
β-strand	168-172	5	6
α-helix	174-179	6
α-helix	182-193	12
α-helix	199-201	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Melanoma-associated antigen 3	A, B, C	protein	209	Homo sapiens	P43357 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9BD2_1 Melanoma-associated antigen 3 (chains A, B, C)
SMEFQAALSRKVAELVHFLLLKYRAREPVTKAEMLGSVVGNWQYFFPVIFSKASSSLQLV
FGIELMEVDPIGHLYIFATCLGLSYDGLLGDNQIMPKAGLLIIVLAIIAREGDCAPEEKI
WEELSVLEVFEGREDSILGDPKKLLTQHFVQENYLEYRQVPGSDPACYEFLWGPRALVET
SYVKVLHHMVKISGGPHISYPPLHEWVLR

Ligands and cofactors

ID	Name	Formula	Copies
A1AL3	(furan-2-yl)[4-({(5P)-5-(1H-indazol-4-yl)-2-[3-(morpholin-4-yl)propoxy]phenyl}m…	C30 H35 N5 O4	1

Primary citation

Development of Ligands and Degraders Targeting MAGE-A3. Li, K., Krone, M.W., Butrin, A. et al. J Am Chem Soc (2024) 146:24884-24891. DOI 10.1021/jacs.4c05393 · PubMed

Other PDB entries of the same protein (UniProt P43357 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V0P 2.07 Å, Crystal structure of the MAGE homology domain of human MAGE-A3
1QEW 2.2 Å, Human class I histocompatibility antigen (HLA-a 0201) complex with a nonameric peptide…
9YTF 2.6 Å, TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
5BRZ 2.62 Å, MAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1
8T9A 3.17 Å, CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3

Browse structure collections

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