SMTL ID : 5jii.1

Crystal structure of human IgG1-Fc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-BMA-MAN-NAG-MAN.1: 11 residues within 4Å: Chain A: F.17, F.19, K.22, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.22

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- FUC: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-FUC.2: 15 residues within 4Å: Chain B: F.17, F.19, P.20, P.21, K.22, E.34, V.35, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.22, B:K.22, B:K.22, B:E.34, B:T.36, B:T.36 Water bridges: B:D.25, B:T.32

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: K.146, D.175, S.176, D.177 Chain B: Q.138, N.166, K.185, T.187 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.187, B:T.187, A:D.177, A:D.177 Water bridges: B:N.166, B:K.185, B:T.187, A:K.146, A:K.146 Salt bridges: B:K.185, A:K.146 PO4.7: 8 residues within 4Å: Chain A: Q.138, N.166, K.185, T.187 Chain B: K.146, D.175, S.176, D.177 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Q.138, A:N.166, A:T.187, A:T.187, B:S.176, B:D.177, B:D.177 Water bridges: A:T.187, B:K.146, B:K.146, B:K.146, B:K.146 Salt bridges: A:K.185, B:K.146

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: I.153, A.154, V.155, E.156, T.169, T.170, P.171, P.172, L.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.155, A:V.155 Water bridges: A:I.153, A:I.153, A:T.169, A:T.169 GOL.5: 7 residues within 4Å: Chain A: G.117, Q.118, R.120, Y.149, D.177, G.178, S.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.118 GOL.6: 5 residues within 4Å: Chain A: E.164, N.165, N.166, Y.167, K.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobner, E. et al., Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies. Structure (2017)

Release Date

2017-04-12

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