SMTL ID : 8w4l.1

Crystal structure of closed conformation of human immunoglobulin Fc in presence of EndoSz

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- MAN- NAG- FUC: N-acetyl-alpha-neuraminic acid-(2-6)-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-SIA-MAN-NAG-FUC.1: 15 residues within 4Å: Chain A: F.17, F.19, P.20, P.21, K.22, E.34, T.36, V.40, D.41, Q.71, Y.72, N.73, R.77 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL-FUC.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL-FUC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.72 Hydrogen bonds: A:F.19, A:K.22, A:E.34, A:E.34, A:T.36

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

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL-FUC.2: 16 residues within 4Å: Chain B: F.17, F.19, P.20, P.21, K.22, D.25, E.34, T.36, V.40, D.41, Q.71, N.73, T.75, R.77 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG-FUC.1, NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.73 Hydrogen bonds: B:F.19, B:K.22, B:K.22, B:D.25, B:E.34, B:E.34, B:T.36, B:T.36, B:K.22, B:T.36

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: L.85, Q.87 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: L.85, H.86, Q.87 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, Y.C. et al., Structure-Based High-Efficiency Homogeneous Antibody Platform by Endoglycosidase Sz Provides Insights into Its Transglycosylation Mechanism. Jacs Au (2024)

Release Date

2024-07-03

Peptides

Immunoglobulin gamma-1 heavy chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Immunoglobulin gamma-1 heavy chain

Related Entries With Identical Sequence