7VAZ: Antibody 14A

Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS). Determined by X-ray diffraction at 2.73 Å resolution. Released 31 Aug 2022.

Method: X-ray diffraction
Resolution: 2.73 Å
Organisms: Mus musculus, Homo sapiens
Chains: 9
Atoms: 9,884
Mol. weight: 148.12 kDa
Ligands: NGA
Released: 31 Aug 2022

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

Secondary structure: helices and β-sheets

7VAZ contains 55 α-helices and 135 β-strands across 9 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	11
β-strand	9-12	4	12
β-strand	17-24	8	11
α-helix	31-33	3
β-strand	36-41	6	12
β-strand	45-51	7	12
β-strand	55-56	2	12
α-helix	57	1
β-strand	64-69	6	11
β-strand	72-78	7	11
α-helix	82-84	3
β-strand	86-93	8	12
β-strand	98-100	3	12
β-strand	104-108	5	12
β-strand	114	1	13
α-helix	115-116	2
β-strand	117-121	5	14
α-helix	122-124	3
α-helix	125-129	5
β-strand	132-142	11	14
β-strand	143	1	13
β-strand	148-153	6	15
β-strand	156-157	2	15
β-strand	162-166	5	14
α-helix	167-170	4
β-strand	176-185	10	14
α-helix	186-191	6
β-strand	194-200	7	15
β-strand	208-213	6	15

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	16
β-strand	12-13	2	17
β-strand	19-26	8	16
α-helix	30-32	3
β-strand	34-40	7	18
β-strand	46-52	7	18
β-strand	59-61	3	18
α-helix	63-65	3
β-strand	69-74	6	16
β-strand	79-84	6	16
α-helix	89-91	3
β-strand	93-100	8	18
β-strand	104-107	4	18
β-strand	108	1	16
β-strand	111-113	3	18
β-strand	114-115	2	17
α-helix	118-120	3
β-strand	121	1	19
α-helix	122-123	2
β-strand	124-128	5	20
β-strand	135-136	2	20
β-strand	139-149	11	20
β-strand	150	1	19
β-strand	155-158	4	21
α-helix	159-161	3
β-strand	167-169	3	20
α-helix	170-172	3
β-strand	173-174	2	20
β-strand	180-189	10	20
α-helix	190-194	5
β-strand	199-204	6	21
α-helix	205-207	3
β-strand	209-214	6	21

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-12	4	2
β-strand	18-24	7	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	186-191	6
β-strand	194-200	7	5
β-strand	208-213	6	5

Chain D: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
β-strand	11-13	3	7
β-strand	19-26	8	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	79-84	6	6
α-helix	89-91	3
β-strand	93-100	8	7
β-strand	104-107	4	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	136	1	9
β-strand	139-149	11	9
β-strand	150	1	8
β-strand	155-158	4	10
α-helix	159-161	3
β-strand	163	1	10
β-strand	167-169	3	9
α-helix	170-172	3
β-strand	173-174	2	9
β-strand	180-189	10	9
α-helix	191-194	4
β-strand	198-204	7	10
α-helix	205-207	3
β-strand	209-215	7	10

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4

Chain F: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	22
β-strand	9-12	4	23
β-strand	17-24	8	22
α-helix	31-33	3
β-strand	36-41	6	23
β-strand	45-51	7	23
β-strand	55-56	2	23
α-helix	57	1
β-strand	64-69	6	22
β-strand	72-78	7	22
α-helix	82-84	3
β-strand	86-93	8	23
β-strand	98-100	3	23
β-strand	104-108	5	23
β-strand	114	1	24
α-helix	115-116	2
β-strand	117-121	5	25
α-helix	122-124	3
α-helix	127-129	3
β-strand	132-142	11	25
β-strand	143	1	24
β-strand	147-153	7	26
β-strand	156-157	2	26
β-strand	162-166	5	25
α-helix	167-170	4
β-strand	176-185	10	25
α-helix	186-191	6
β-strand	195-201	7	26
β-strand	208-212	5	26

Chains G and I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3

Chain H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	27
β-strand	12-13	2	28
β-strand	18-26	9	27
α-helix	30-32	3
β-strand	35-40	6	29
β-strand	46-52	7	29
β-strand	59-61	3	29
α-helix	63-65	3
β-strand	69-74	6	27
β-strand	79-85	7	27
α-helix	89-91	3
β-strand	93-100	8	29
β-strand	104-107	4	29
β-strand	111-113	3	29
β-strand	114-115	2	28
α-helix	118-120	3
β-strand	121	1	30
α-helix	122-123	2
β-strand	124-127	4	31
α-helix	136-138	3
β-strand	139-149	11	31
β-strand	150	1	30
β-strand	155-158	4	32
α-helix	159-161	3
β-strand	163	1	32
β-strand	167-169	3	31
α-helix	170-172	3
β-strand	173-174	2	31
β-strand	180-189	10	31
β-strand	193	1	33
β-strand	196	1	33
β-strand	200-204	5	32
α-helix	205-207	3
β-strand	209-213	5	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
14A fab light chain	A, C, F	protein	217	Mus musculus
14A fab heavy chain	B, D, H	protein	229	Mus musculus
Mucin-1 subunit alpha	E, G, I	protein	13	Homo sapiens	P15941 (AlphaFold model)

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

>7VAZ_1 14A fab light chain (chains A, C, F)
QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGRTNNRVPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHFIFGSGTKVTVLKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D, H), FASTA

>7VAZ_2 14A fab heavy chain (chains B, D, H)
MEVKLLQSGGGLVQPGGSLKLSCAASGIDFSGYWMSWVRRAPGKGLEWIGEITPDSSTIN
YAPSLKDEFIISRDNAKNTLYLQMTKVRSDDTALYYCVSYYEGFAYWGQGTLVTVSAAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTENLYFQ

Sequence of entity 3 (E, G, I), FASTA

>7VAZ_3 Mucin-1 subunit alpha (chains E, G, I)
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
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

About this viewer

MolViewer shows 7VAZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.