6FZR: ScFv-SM3

Crystal structure of scFv-SM3 in complex with compound 2. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 Feb 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 1,919
Mol. weight: 27.15 kDa
Ligands: EEQ
Released: 20 Feb 2019

Explore 6FZR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FZR contains 8 α-helices and 23 β-strands across 1 chain. 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 H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	44-51	8	2
α-helix	54-56	3
β-strand	60-62	3	2
α-helix	64-66	3
β-strand	70-75	6	1
α-helix	76-78	3
β-strand	80-85	6	1
α-helix	90-92	3
β-strand	94-100	7	2
β-strand	108-109	2	2
β-strand	113-117	5	2
β-strand	1011-1013	3	3
β-strand	1016-1019	4	4
β-strand	1024-1031	8	3
β-strand	1034	1	3
α-helix	1038-1040	3
β-strand	1043-1048	6	4
β-strand	1052-1058	7	4
β-strand	1062-1063	2	4
α-helix	1064	1
β-strand	1071-1076	6	3
β-strand	1079-1085	7	3
α-helix	1089-1091	3
β-strand	1093-1100	8	4
β-strand	1105-1107	3	4
β-strand	1111-1115	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
scFv-SM3	H	protein	244	Mus musculus
Mucin-1	P	protein	6	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6FZR_1 scFv-SM3 (chains H)
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSSSG
GGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLF
TGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL
TVLG

Sequence of entity 2 (P), FASTA

>6FZR_2 Mucin-1 (chains P)
APDTRP

Ligands and cofactors

ID	Name	Formula	Copies
EEQ	2-deoxy-2-[(fluoroacetyl)amino]-alpha-D-galactopyranose	C8 H14 F N O6	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Water Sculpts the Distinctive Shapes and Dynamics of the Tumor-Associated Carbohydrate Tn Antigens: Implications for Their Molecular Recognition. Bermejo, I.A., Usabiaga, I., Companon, I. et al. J Am Chem Soc (2018) 140:9952-9960. DOI 10.1021/jacs.8b04801 · 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
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

Browse structure collections

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