Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP. Determined by X-ray diffraction at 1.79 Å resolution. Released 3 Jun 2015.
Explore 5A2L in 3D Show helices and sheets RCSB PDB PDBe
5A2L 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.
| 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 | 52B-53 | 3 | |
| β-strand | 57-59 | 3 | 2 |
| α-helix | 61-63 | 3 | |
| 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 |
| β-strand | 1027A | 1 | 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 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| scFv-SM3 | H | protein | 244 | MUS MUSCULUS | P01727 (AlphaFold model), P01801 (AlphaFold model) |
| Modified antigen tn | P | protein | 6 | HOMO SAPIENS |
>5A2L_1 SCFV-SM3 (chains H) QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYAT HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSASSG GGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLF TGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL TVLG
>5A2L_2 MODIFIED ANTIGEN TN (chains P) APDCRP
| 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.
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:
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