7V4W: Antibody 16A

Crystal structure of Antibody 16A in complex with MUC1 peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 17 Aug 2022.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,574
Mol. weight: 49.51 kDa
Released: 17 Aug 2022

Explore 7V4W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V4W contains 19 α-helices and 43 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-12	4	2
β-strand	17-24	8	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	72-78	7	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
α-helix	158	1
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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
β-strand	11-13	3	7
β-strand	18-26	9	6
α-helix	30-32	3
β-strand	35-40	6	7
β-strand	46-52	7	7
β-strand	59-61	3	7
α-helix	63-65	3
β-strand	69-74	6	6
α-helix	75-77	3
β-strand	79-85	7	6
α-helix	89-91	3
β-strand	93-101	9	7
β-strand	103-107	5	7
β-strand	111-115	5	7
α-helix	118-120	3
β-strand	121	1	8
α-helix	122-123	2
β-strand	124-128	5	9
β-strand	140-149	10	9
β-strand	150	1	8
β-strand	155-158	4	10
α-helix	159-161	3
β-strand	167-169	3	9
α-helix	170-172	3
β-strand	173-174	2	9
β-strand	180-188	9	9
β-strand	199-204	6	10
α-helix	205-207	3
β-strand	209-214	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

>7V4W_1 16A Fab Light chain (chains A)
QAVVTQESALTTSPGETVTLTCRSSTGAVITSNYANWVQEKPDHLFTGLIGRTYNRVPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHFVFGGGTKLTVLKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>7V4W_2 16A Fab Heavy chain (chains B)
MEVKLHQSGGGLVQPGGFLKISCVVSGIDFSRYWMSWVRRAPGKGLEWIGEITPDSNTIN
YVPSLKDNFGISRDNAKNTLFLQMTKVRSEDTALYFCASYYEGFAYWGQGTLVTVSAAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTENLYFQ

Sequence of entity 3 (C), FASTA

>7V4W_3 Mucin-1 subunit alpha (chains C)
RPAPGSTAPPAHG

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

Browse structure collections

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