SMTL ID : 6gfe.1

High-resolution Structure of a therapeutic full-length anti-NPRA Antibody with exceptional Conformational Diversity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- MAN- FUC: 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-MAN-FUC.1: 15 residues within 4Å: Chain A: F.244, F.246, K.249, T.263, V.267, D.268, Q.298, N.300, T.302, R.304 Chain C: R.109, T.110, D.171 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-FUC.2 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:T.110, C:T.110, A:K.249, A:K.249 Water bridges: A:F.299, A:T.263, A:R.304, A:R.304 NAG-NAG-BMA-MAN-NAG-MAN-FUC.2: 12 residues within 4Å: Chain B: F.244, F.246, K.249, T.263, V.265, V.267, D.268, Q.298, N.300, T.302, R.304 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-FUC.1 5 PLIP interactions: 5 interactions with chain B Water bridges: B:F.299, B:T.263, B:T.263, B:R.304 Hydrogen bonds: B:K.249, B:K.249

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: S.33, D.103 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.33, A:D.103, H2O.1, H2O.11, H2O.13 CA.4: 1 residues within 4Å: Chain B: E.433 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.433, H2O.19, H2O.19, H2O.19, H2O.33

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

ACT.5: 5 residues within 4Å: Chain B: Y.109, D.111 Chain D: Y.50, A.56, T.57 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.109, B:D.111, D:T.57 Hydrophobic interactions: D:Y.50 ACT.6: 5 residues within 4Å: Chain A: Y.109 Chain C: L.47, Y.50, A.56, T.57 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.47, C:Y.50, A:Y.109 Hydrogen bonds: C:T.57, C:T.57 ACT.7: 2 residues within 4Å: Chain C: Q.6, S.7 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.7, C:S.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blech, M. et al., Structure of a Therapeutic Full-Length Anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity. Biophys.J. (2019)

Release Date

2019-05-15

Peptides

Immunoglobulin gamma-4 heavy chain: AB
Immunoglobulin gamma-4 light chain: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
K

C
L

D
M

Immunoglobulin gamma-4 heavy chain

Immunoglobulin gamma-4 light chain