7V7K: Antibody 16A

Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoST). Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Aug 2022.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,605
Mol. weight: 49.95 kDa
Ligands: NGA
Released: 24 Aug 2022

Explore 7V7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V7K contains 19 α-helices and 47 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	4-5	2	1
β-strand	9-12	4	2
β-strand	18-22	5	3
β-strand	23-24	2	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	3
β-strand	72-77	6	3
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	4
α-helix	115-116	2
β-strand	117-121	5	5
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	5
β-strand	143	1	4
β-strand	147-153	7	6
β-strand	157	1	6
β-strand	162-166	5	5
α-helix	167-170	4
β-strand	176-185	10	5
α-helix	186-190	5
β-strand	194-201	8	6
β-strand	208-213	6	6

Chain B: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	7
β-strand	11-13	3	8
β-strand	19-26	8	7
α-helix	30-32	3
β-strand	35-41	7	8
β-strand	45-52	8	8
β-strand	59-61	3	8
α-helix	63-65	3
β-strand	69-74	6	7
β-strand	79-84	6	7
α-helix	89-91	3
β-strand	93-101	9	8
β-strand	103-107	5	8
β-strand	111-115	5	8
α-helix	118-120	3
β-strand	121	1	9
α-helix	122-123	2
β-strand	124-128	5	10
α-helix	132-134	3
β-strand	135	1	10
β-strand	140-149	10	10
β-strand	150	1	9
β-strand	155-158	4	11
α-helix	159-161	3
β-strand	163	1	11
β-strand	167-169	3	10
α-helix	170-172	3
β-strand	173-174	2	10
β-strand	180-188	9	10
α-helix	190-192	3
β-strand	193	1	12
β-strand	196	1	12
β-strand	199-204	6	11
α-helix	205-207	3
β-strand	209-214	6	11

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

>7V7K_1 16A fab light chain (chains A)
QAVVTQESALTTSPGETVTLTCRSSTGAVITSNYANWVQEKPDHLFTGLIGRTYNRVPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHFVFGGGTKLTVLKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>7V7K_2 16A fab heavy chain (chains B)
MEVKLHQSGGGLVQPGGFLKISCVVSGIDFSRYWMSWVRRAPGKGLEWIGEITPDSNTIN
YVPSLKDNFGISRDNAKNTLFLQMTKVRSEDTALYFCASYYEGFAYWGQGTLVTVSAAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTENLYFQ

Sequence of entity 3 (C), FASTA

>7V7K_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	2

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
7V64 1.56 Å, Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
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

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