SMTL ID : 3d6g.1

Fc fragment of IgG1 (Herceptin) with protein-A mimetic peptide dendrimer ligand.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1: 12 residues within 4Å: Chain A: F.6, F.8, K.11, T.25, V.29, D.30, Q.60, N.62, T.64, R.66 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60, A:K.11, A:K.11 Water bridges: A:Y.61, A:R.66, A:R.66 NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2: 11 residues within 4Å: Chain B: F.6, F.8, K.11, T.25, V.29, D.30, Q.60, N.62, T.64, R.66 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.66, B:K.11, B:K.11

1 x X12: 2-[[(2S)-2,6-bis[[(2S)-2,6-bis[[(2R)-2-[[(2R,3R)-2-[[(2R)-2-amino-5-carbamimidamido-pentanoyl]amino]-3-hydroxy-butanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]hexanoyl]amino]hexanoyl]amino]ethanoic acid(Non-covalent)

X12.3: 8 residues within 4Å: Chain B: T.15, L.16, M.17, I.18, H.75, Q.76, L.79, H.200 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.18 Hydrogen bonds: B:L.16, B:Q.76 Water bridges: B:Q.76, B:N.199 Salt bridges: B:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moiani, D. et al., Structural characterization of a Protein A mimetic peptide dendrimer bound to human IgG. J.Phys.Chem.B (2009)

Release Date

2009-06-16

Peptides

Ig gamma-1 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ig gamma-1 chain C region

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