SMTL ID : 8w4m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

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.1: 14 residues within 4Å: Chain A: F.17, L.18, F.19, P.20, K.22, E.34, T.36, V.38, V.40, D.41, Q.71, N.73, T.75, R.77 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.19, A:E.34, A:E.34 Water bridges: A:D.25, A:E.34

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.86, L.90, H.211 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.86, A:H.211, H2O.4, H2O.4, H2O.5 ZN.3: 2 residues within 4Å: Chain A: E.94, T.111 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.94, A:E.94 ZN.4: 1 residues within 4Å: Chain A: H.61 No protein-ligand interaction detected (PLIP) ZN.5: 1 residues within 4Å: Chain A: E.121 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.121, A:E.121, H2O.1, H2O.2, H2O.4 ZN.6: 6 residues within 4Å: Chain A: D.88, W.89, G.92, K.93, S.113, K.114 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:W.89, A:K.93 ZN.7: 4 residues within 4Å: Chain A: T.26, H.86, W.89, L.90 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.26, A:H.86 ZN.8: 3 residues within 4Å: Chain A: L.85, D.88, Y.95 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.88, A:Y.95 ZN.9: 2 residues within 4Å: Chain A: E.59, H.61 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.59, A:H.61 ZN.10: 1 residues within 4Å: Chain A: H.209 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.209, H2O.5 ZN.11: 1 residues within 4Å: Chain A: E.156 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.156, A:E.156

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Immunoglobulin gamma-1 heavy chain

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