SMTL ID : 5a2j.1

Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- THR- ARG- PRO: THE NAKED PEPTIDE APDTRP(Non-covalent)

ALA-PRO-ASP-THR-ARG-PRO.1: 7 residues within 4Å: Chain A: N.31, Y.32, W.33, Q.103, Y.168, W.227, W.232 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.32, A:W.33, A:Y.168, A:Y.168, A:Y.168, A:W.227, A:W.232 Hydrogen bonds: A:Y.32, A:W.33, A:Q.103 Water bridges: A:N.31, A:N.31, A:Y.32, A:W.33, A:R.52, A:G.102

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: I.95, Q.109, G.110, T.111, T.112 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.109, A:T.112, A:T.112 Water bridges: A:T.111, A:T.112 EDO.3: 6 residues within 4Å: Chain A: L.45, E.46, W.47, W.232, V.233, F.234 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.45, A:W.47, A:W.232, A:F.234 EDO.4: 3 residues within 4Å: Chain A: L.144, V.152, T.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.151, A:T.153 EDO.5: 4 residues within 4Å: Chain A: Q.13, P.14, G.15, G.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.14 Water bridges: A:Q.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Saez, N. et al., Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-06-03

Peptides

SCFV-SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

SCFV-SM3

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