SMTL ID : 5vh5.1

Crystal Structure of Fc fragment of anti-TNFa antibody infliximab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- FUL: 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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN-FUL.1: 14 residues within 4Å: Chain A: F.49, F.51, P.52, P.53, K.54, E.66, T.68, V.70, V.72, D.73, Q.103, N.105, T.107, R.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.103, A:P.52, A:K.54, A:E.66, A:E.66, A:T.68 Water bridges: A:Y.104, A:D.57 NAG-NAG-BMA-MAN-NAG-GAL-MAN-FUL.6: 14 residues within 4Å: Chain B: F.49, F.51, P.52, P.53, K.54, E.66, T.68, V.70, V.72, D.73, Q.103, N.105, T.107, R.109 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.103, B:P.52, B:K.54, B:E.66, B:E.66, B:E.66 Water bridges: B:Y.104, B:D.57, B:D.57

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.118, L.122, H.243 Ligands: ACT.5 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.118, A:H.243, H2O.2, H2O.6, ACT.5 ZN.3: 1 residues within 4Å: Chain A: H.93 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, H2O.6 ZN.4: 3 residues within 4Å: Chain A: E.126 Chain B: E.126 Ligands: ZN.9 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.126, B:E.126, A:E.126, A:E.126, H2O.13 ZN.7: 4 residues within 4Å: Chain B: H.118, L.122, H.243 Ligands: ACT.10 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.118, B:H.243, H2O.9, H2O.14, ACT.10 ZN.8: 1 residues within 4Å: Chain B: H.93 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.93, H2O.14 ZN.9: 3 residues within 4Å: Chain A: E.126 Chain B: E.126 Ligands: ZN.4 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.126, B:E.126, A:E.126, A:E.126, H2O.6

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain A: H.118, Q.119, L.122, H.243 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.119 Salt bridges: A:H.118, A:H.243 ACT.10: 5 residues within 4Å: Chain B: H.118, Q.119, L.122, H.243 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.119 Salt bridges: B:H.118, B:H.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lerch, T.F. et al., Infliximab crystal structures reveal insights into self-association. MAbs (2017)

Release Date

2017-05-03

Peptides

Infliximab Fc: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Infliximab Fc

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