7V64: Antibody 16A

Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT). Determined by X-ray diffraction at 1.56 Å resolution. Released 24 Aug 2022.

Method: X-ray diffraction
Resolution: 1.56 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,835
Mol. weight: 49.73 kDa
Ligands: NGA
Released: 24 Aug 2022

Explore 7V64 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V64 contains 19 α-helices and 46 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-12	4	2
β-strand	18-24	7	1
β-strand	27	1	1
α-helix	31-33	3
β-strand	36-41	6	2
β-strand	45-51	7	2
β-strand	55-56	2	2
α-helix	57	1
β-strand	64-69	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-93	8	2
β-strand	98-100	3	2
β-strand	104-108	5	2
β-strand	114	1	3
α-helix	115-116	2
β-strand	117-121	5	4
α-helix	122-124	3
α-helix	125-129	5
β-strand	132-142	11	4
β-strand	143	1	3
β-strand	148-153	6	5
β-strand	156-157	2	5
β-strand	162-166	5	4
α-helix	167-170	4
β-strand	176-185	10	4
α-helix	186-189	4
β-strand	194-200	7	5
β-strand	208-213	6	5

Chain B: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-100	9	7
β-strand	102-106	5	7
β-strand	110-114	5	7
α-helix	117-119	3
β-strand	120	1	8
α-helix	121-122	2
β-strand	123-127	5	9
β-strand	138-148	11	9
β-strand	149	1	8
β-strand	154-157	4	10
α-helix	158-160	3
β-strand	162	1	10
β-strand	166-168	3	9
α-helix	169-171	3
β-strand	172-173	2	9
β-strand	179-188	10	9
α-helix	189-191	3
β-strand	192	1	11
β-strand	195	1	11
β-strand	198-203	6	10
α-helix	204-206	3
β-strand	208-213	6	10

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
16A fab Light chain	A	protein	217	Mus musculus
16A fab Heavy chain	B	protein	229	Mus musculus
Mucin-1 subunit alpha	C	protein	13	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7V64_1 16A fab Light chain (chains A)
QAVVTQESALTTSPGETVTLTCRSSTGAVITSNYANWVQEKPDHLFTGLIGRTYNRVPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHFVFGGGTKLTVLKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>7V64_2 16A fab Heavy chain (chains B)
MEVKLHQSGGGLVQPGGFLKISCVVSGIDFSRYWMSWVRRAPGKGLEWIGEITPDSNTIN
YVPSLKDNFGISRDNAKNTLFLQMTKVRSEDTALYFCASYYEGFAYWGQGTLVTVSAAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTENLYFQ

Sequence of entity 3 (C), FASTA

>7V64_3 Mucin-1 subunit alpha (chains C)
RPAPGSTAPPAHG

Ligands and cofactors

ID	Name	Formula	Copies
NGA	2-acetamido-2-deoxy-beta-D-galactopyranose	C8 H15 N O6	1

Primary citation

Site-specific GalNAc modification on a MUC1 neoantigen epitope forms a basis for high-affinity antibody binding. Han, Y.B., Xu, L. To be published.

Other PDB entries of the same protein (UniProt P15941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSC 1.3 Å, Crystal structure of the Mucin-1 SEA domain
6BSB 1.6 Å, Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
6FZQ 1.7 Å, Crystal structure of scFv-SM3 in complex with compound 3
8S6K 1.75 Å, Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
6KX1 1.77 Å, Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide
6FZR 1.8 Å, Crystal structure of scFv-SM3 in complex with compound 2
8AXH 1.85 Å, Crystal structure of a MUC1-like glycopeptide containing the unnatural…
8S6T 1.85 Å, Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
8S6V 1.95 Å, Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide
5T6P 1.97 Å, Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
6TGG 2.0 Å, scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

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