SMTL ID : 4bsw.1

Heterodimeric Fc Antibody Azymetric Variant 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1: 16 residues within 4Å: Chain A: F.20, F.22, P.23, P.24, K.25, E.37, T.39, V.43, D.44, Q.74, Y.75, N.76, T.78, R.80, K.113 Ligands: EDO.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.75, A:N.76 Hydrogen bonds: A:F.22, A:K.25, A:K.25, A:E.37, A:E.37, A:E.37, A:T.39, A:T.39 Water bridges: A:D.28 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2: 17 residues within 4Å: Chain B: F.20, F.22, P.23, P.24, K.25, D.28, E.37, T.39, V.41, V.43, D.44, Q.74, Y.75, N.76, T.78, R.80 Ligands: EDO.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.75 Hydrogen bonds: B:F.22, B:K.25, B:K.25, B:D.28, B:E.37, B:E.37, B:T.39, B:T.39 Water bridges: B:D.28

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

EDO.3: 7 residues within 4Å: Chain A: T.29, L.30, I.32, H.89, Q.90, L.93, H.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.214 Water bridges: A:L.30, A:L.30, A:I.32, A:I.32 EDO.5: 2 residues within 4Å: Chain A: P.23 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.1 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain B: I.156, A.157, V.158 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.158, B:V.158 EDO.8: 5 residues within 4Å: Chain B: F.20, L.21, K.113 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.21, B:K.113, B:K.113 EDO.9: 6 residues within 4Å: Chain B: P.26, S.154, D.155, I.156, P.175 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.155, B:D.155, B:I.156

3 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 2 residues within 4Å: Chain A: K.27, R.34 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: I.32, S.33 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain B: M.31, I.32, S.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Von Kreudenstein, T.S. et al., Improving Biophysical Properties of a Bispecific Antibody Scaffold to Aid Developability: Quality by Molecular Design. Mabs (2013)

Release Date

2013-08-21

Peptides

HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2: A
HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2

HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2

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