SMTL ID : 5iw3.1

anti-CD20 monoclonal antibody Fc fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1: 16 residues within 4Å: Chain A: F.6, F.8, P.9, P.10, K.11, D.14, E.23, T.25, V.29, D.30, Q.60, N.62, T.64, R.66 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.7, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.8, A:D.14, A:D.14, A:E.23, A:E.23, A:T.25, A:T.25 Water bridges: A:K.11 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.7: 16 residues within 4Å: Chain B: F.6, F.8, P.9, P.10, K.11, D.14, E.23, T.25, V.29, D.30, Q.60, N.62, T.64, R.66 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.8, B:D.14, B:E.23, B:E.23, B:T.25 Water bridges: B:K.11

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: N.126, D.178, K.179, S.180 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.178, A:K.179, A:S.180, A:S.180, A:S.180 SO4.3: 3 residues within 4Å: Chain A: H.33, E.59, Y.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.59 Salt bridges: A:H.33 SO4.4: 2 residues within 4Å: Chain A: K.85, E.98 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.87, A:E.98 Salt bridges: A:K.85, A:K.87 SO4.8: 4 residues within 4Å: Chain B: N.126, D.178, K.179, S.180 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.178, B:D.178, B:K.179, B:S.180, B:S.180, B:S.180 SO4.9: 3 residues within 4Å: Chain B: H.33, E.59, Y.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.59, B:Y.65 Water bridges: B:E.59 Salt bridges: B:H.33 SO4.10: 2 residues within 4Å: Chain B: K.85, E.98 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.87, B:E.98 Salt bridges: B:K.85, B:K.87

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

ACT.5: 5 residues within 4Å: Chain A: F.40, A.52, K.53, T.54, S.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.54 Water bridges: A:F.40, A:T.54 ACT.6: 1 residues within 4Å: Chain A: E.110 No protein-ligand interaction detected (PLIP) ACT.11: 5 residues within 4Å: Chain B: F.40, A.52, K.53, T.54, S.69 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.40, B:T.54 ACT.12: 1 residues within 4Å: Chain B: E.110 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, C. et al., Structure of anti-CD20 monoclonal antibody Fc fragment at 2.05 Angstroms resolution. To Be Published

Release Date

2017-03-29

Peptides

Ig gamma-1 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ig gamma-1 chain C region