5T78: Therapeutic mAB AR20.5

Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 11 Jan 2017.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 6,727
Mol. weight: 96.24 kDa
Ligands: NGA
Released: 11 Jan 2017

Explore 5T78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T78 contains 29 α-helices and 89 β-strands across 6 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: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27	1	3
β-strand	30	1	4
β-strand	36	1	4
β-strand	38-43	6	2
β-strand	49-54	6	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-95	7	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-112	6	2
β-strand	116	1	5
β-strand	119-123	5	6
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	6
β-strand	145	1	5
β-strand	150-155	6	7
β-strand	158-160	3	7
β-strand	164-168	5	6
α-helix	169-172	4
β-strand	178-187	10	6
α-helix	188-192	5
β-strand	196-203	8	7
β-strand	206-215	10	7

Chain B: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	59	1	9
β-strand	69-73	5	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	103-106	4	9
β-strand	110-114	5	9
β-strand	120	1	10
α-helix	121-122	2
β-strand	123-127	5	11
β-strand	138-148	11	11
β-strand	149	1	10
β-strand	154-157	4	12
α-helix	158-160	3
β-strand	166-168	3	11
α-helix	169-171	3
β-strand	172-174	3	11
β-strand	177-187	11	11
β-strand	197-202	6	12
α-helix	203-205	3
β-strand	207-212	6	12

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	30	1	15
β-strand	36	1	15
β-strand	38-43	6	14
β-strand	49-54	6	14
β-strand	58-59	2	14
α-helix	60	1
β-strand	67-72	6	13
β-strand	75-80	6	13
α-helix	85-87	3
β-strand	89-95	7	14
α-helix	101	1
β-strand	102-103	2	14
β-strand	107-112	6	14
β-strand	116	1	16
β-strand	119-123	5	3
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	3
β-strand	145	1	16
β-strand	150-155	6	17
β-strand	158-160	3	17
β-strand	164-168	5	3
α-helix	169-172	4
β-strand	178-187	10	3
α-helix	188-192	5
β-strand	196-203	8	17
β-strand	206-215	10	17

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	59	1	19
β-strand	69-73	5	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	103-106	4	19
β-strand	110-114	5	19
α-helix	117-119	3
β-strand	120	1	20
α-helix	121-122	2
β-strand	123-127	5	21
β-strand	138-148	11	21
β-strand	149	1	20
β-strand	154-157	4	22
α-helix	158-160	3
β-strand	166-168	3	21
α-helix	169-171	3
β-strand	172-174	3	21
β-strand	177-187	11	21
β-strand	197-202	6	22
α-helix	203-205	3
β-strand	207-212	6	22

Chains E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment AR20.5 - Light Chain	A, C	protein	216	Mus musculus
Fab Fragment - AR20.5 - Heavy chain	B, D	protein	215	Mus musculus
MUC1 Glycopeptide	E, F	protein	8	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5T78_1 Fab fragment AR20.5 - Light Chain (chains A, C)
DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGKIYLEWYLQKPGQSPKLLIYRVSKRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (B, D), FASTA

>5T78_2 Fab Fragment - AR20.5 - Heavy chain (chains B, D)
EVKLVESGGGLVAPGGSLKLSCAASGFTFSSYPMSWVRQTPEKRLEWVAYINNGGGNPYY
PDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAIYYCIRQYYGFDYWGQGTTLTVSSAKTT
PPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Sequence of entity 3 (E, F), FASTA

>5T78_3 MUC1 Glycopeptide (chains E, F)
APDTRPAP

Ligands and cofactors

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

Primary citation

Glycosylation of MUC1 influences the binding of a therapeutic antibody by altering the conformational equilibrium of the antigen. Movahedin, M., Brooks, T.M., Supekar, N.T. et al. Glycobiology (2017) 27:677-687. DOI 10.1093/glycob/cww131 · PubMed

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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