5A2I: ScFv-SM3

Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP. Determined by X-ray diffraction at 1.88 Å resolution. Released 3 Jun 2015.

Method: X-ray diffraction
Resolution: 1.88 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS
Chains: 2
Atoms: 1,838
Mol. weight: 26.73 kDa
Ligands: A2G
Released: 3 Jun 2015

Explore 5A2I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5A2I contains 7 α-helices and 22 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, 22 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	34-38	5	2
β-strand	46-51	6	2
α-helix	52B-53	3
β-strand	57-59	3	2
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	1005-1007	3	3
β-strand	1010-1013	4	4
β-strand	1018-1025	8	3
α-helix	1029-1031	3
β-strand	1034-1039	6	4
β-strand	1043-1049	7	4
β-strand	1053-1054	2	4
α-helix	1055	1
β-strand	1062-1067	6	3
β-strand	1070-1076	7	3
α-helix	1080-1082	3
β-strand	1084-1091	8	4
β-strand	1096-1098	3	4
β-strand	1102-1106	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ig lambda-1 chain V region S43	H	protein	244	MUS MUSCULUS	P01727 (AlphaFold model), P01801 (AlphaFold model)
Antigen tn, ser is covalently bound to galnac	P	protein	6	HOMO SAPIENS

Sequence of entity 1 (H), FASTA

>5A2I_1 IG LAMBDA-1 CHAIN V REGION S43 (chains H)
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSASSG
GGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLF
TGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL
TVLG

Sequence of entity 2 (P), FASTA

>5A2I_2 ANTIGEN TN, SER IS COVALENTLY BOUND TO GALNAC (chains P)
APDSRP

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

Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody. Martinez-Saez, N., Castro-Lopez, J., Valero-Gonzalez, J. et al. Angew Chem Int Ed Engl (2015) 54:9830. DOI 10.1002/ANIE.201502813 · 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
5N7B 1.7 Å, Understanding the singular conformational landscape of the Tn antigens: Sulfur-for-…
5A2L 1.79 Å, Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP

Browse structure collections

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