SMTL ID : 4bsv.1

Heterodimeric Fc Antibody Azymetric Variant 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 6 residues within 4Å: Chain A: D.44, Q.74, Y.75, N.76, T.78 Ligands: NAG-BMA-MAN-NAG-GAL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.44, A:N.76 Water bridges: A:D.44, A:D.44, A:D.44, A:T.78

1 x NAG- BMA- MAN- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN-NAG-GAL.2: 13 residues within 4Å: Chain A: F.20, F.22, P.23, K.25, E.37, T.39, V.41, V.43, R.80 Ligands: NAG-FUC.1, NAG-FUC.1, MAN-NAG.3, EDO.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.25, A:F.22, A:K.25, A:E.37, A:E.37, A:E.37, A:T.39 Water bridges: A:R.80, A:D.28, A:D.28, A:E.37, A:E.37

1 x MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-NAG.3: 2 residues within 4Å: Chain A: F.20 Ligands: NAG-BMA-MAN-NAG-GAL.2 No protein-ligand interaction detected (PLIP)

1 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.4: 15 residues within 4Å: Chain B: F.20, F.22, P.23, P.24, K.25, E.37, T.39, V.41, V.43, D.44, Q.74, Y.75, N.76, T.78, R.80 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.75 Water bridges: B:Y.75, B:E.37 Hydrogen bonds: B:F.22, B:K.25, B:E.37, B:E.37, B:T.39, B:T.39

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

EDO.5: 4 residues within 4Å: Chain A: I.156, A.157, V.158, L.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.158, A:V.158 EDO.6: 3 residues within 4Å: Chain A: F.22, P.23 Ligands: NAG-BMA-MAN-NAG-GAL.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.23 EDO.7: 6 residues within 4Å: Chain A: Q.141 Chain B: K.149, D.178, S.179, D.180 Ligands: EDO.13 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.188, B:D.178 Water bridges: A:Q.141, A:Q.141, B:K.149, B:K.149, B:K.149, B:S.182 EDO.8: 5 residues within 4Å: Chain A: E.51, K.53, S.103, N.104, K.105 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.105 EDO.9: 3 residues within 4Å: Chain B: K.27, S.33, R.34 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.27, B:R.34, B:R.34 Water bridges: B:S.33, B:S.33 EDO.10: 4 residues within 4Å: Chain B: A.157, V.158, T.172 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.158, B:V.158 EDO.11: 1 residues within 4Å: Chain B: G.164 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain B: P.26, S.154, D.155, I.156 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.154, B:I.156 EDO.13: 6 residues within 4Å: Chain A: Q.141, K.188, T.190 Chain B: K.149, D.178 Ligands: EDO.7 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Water bridges: A:K.188, A:K.188, A:T.190, A:T.190, A:T.190 Hydrogen bonds: B:K.149, B:K.149, B:K.149

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

IOD.14: 3 residues within 4Å: Chain B: M.31, S.33 Ligands: IOD.15 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain B: M.31, S.33 Ligands: IOD.14 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain B: G.164 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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