5N7B: PDB entry 5N7B

Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Jun 2018.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Mus musculus, synthetic construct
Chains: 2
Atoms: 2,081
Mol. weight: 27.08 kDa
Ligands: A2G
Released: 27 Jun 2018

Explore 5N7B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N7B contains 7 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: 7 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
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	1093-1101	9	4
β-strand	1104-1107	4	4
β-strand	1111-1115	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43	H	protein	244	Mus musculus	P01727 (AlphaFold model), P01801 (AlphaFold model)
APD(CG6)RP(NH2) peptide	I	protein	7	synthetic construct

Sequence of entity 1 (H), FASTA

>5N7B_1 Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43 (chains H)
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSSSG
GGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLF
TGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL
TVLG

Sequence of entity 2 (I), FASTA

>5N7B_2 APD(CG6)RP(NH2) peptide (chains I)
APDCRPX

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	1

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

Primary citation

Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage. Companon, I., Guerreiro, A., Mangini, V. et al. J Am Chem Soc (2019) 141:4063-4072. DOI 10.1021/jacs.8b13503 · PubMed

Other PDB entries of the same protein (UniProt P01727 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5A2J 1.65 Å, Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP
5A2K 1.7 Å, Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP
5A2L 1.79 Å, Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP
5A2I 1.88 Å, Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP

Browse structure collections

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