SMTL ID : 5vu0.1

Crystal structure of the complex between afucosylated/galactosylated human IgG1 Fc and Fc gamma receptor IIIa (CD16A) with Man5 N-glycans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-2-1-mer

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: 19 residues within 4Å: Chain A: F.14, F.16, P.17, P.18, K.19, E.31, T.33, V.35, V.37, D.38, Q.68, N.70, T.72, R.74 Chain C: T.120, Y.130 Ligands: PEG.6, PEG.7, NAG.19 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.16, A:K.19, A:E.31, A:E.31 Water bridges: A:K.19, A:E.31 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.2: 14 residues within 4Å: Chain B: F.14, F.16, P.17, P.18, K.19, E.31, T.33, V.35, V.37, D.38, Q.68, N.70, T.72, R.74 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:F.16, B:K.19, B:K.19, B:E.31, B:E.31, B:T.33 Water bridges: B:D.22, B:D.22

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: P.18, T.23, W.86, K.111, D.149, E.203 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: Y.146, P.147, S.148, D.149, F.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.148 EDO.13: 5 residues within 4Å: Chain B: P.119, Q.120, V.121, Y.122, K.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.119, B:V.121, B:Y.122 EDO.21: 6 residues within 4Å: Chain C: W.14, Y.15, R.16, Q.92, A.93, W.96 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.16, C:R.16, C:A.93, C:W.96 EDO.22: 5 residues within 4Å: Chain C: G.87, W.88, L.89, S.162, S.163 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.88, C:L.89, C:L.89

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 7 residues within 4Å: Chain A: I.150, A.151, V.152, T.166, T.167, P.168, P.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.152, A:T.167 PEG.6: 7 residues within 4Å: Chain A: F.16, P.17, P.18, K.19 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.19 PEG.7: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 No protein-ligand interaction detected (PLIP) PEG.14: 8 residues within 4Å: Chain B: P.20, S.148, D.149, I.150, T.166, T.167, P.169, L.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.148, B:I.150 Water bridges: B:D.149

9 x NA: SODIUM ION(Non-functional Binders)

NA.8: 7 residues within 4Å: Chain A: P.126, S.127, E.130, S.137 Chain B: L.124, L.141 Ligands: NA.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.127, A:S.137 NA.9: 5 residues within 4Å: Chain A: W.86, G.89, K.90, S.110, K.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.89, A:G.89, A:K.111 NA.10: 6 residues within 4Å: Chain A: P.11, S.40, D.43, N.98, A.100 Chain C: H.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.40, A:N.98, A:N.98 Water bridges: A:D.43 NA.11: 5 residues within 4Å: Chain A: W.190, G.193, N.194, S.215, L.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.193, A:G.193, A:L.216 NA.12: 8 residues within 4Å: Chain A: L.124, P.125, P.126, S.137, L.138, T.139 Chain B: L.124 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.124, A:T.139 NA.15: 7 residues within 4Å: Chain A: L.124 Chain B: L.124, P.125, P.126, S.137, T.139 Ligands: NA.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.137 NA.16: 5 residues within 4Å: Chain B: W.86, G.89, K.90, S.110, K.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.89, B:G.89, B:K.111 NA.17: 5 residues within 4Å: Chain B: W.190, G.193, N.194, S.215, L.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.190, B:G.193, B:L.216 NA.18: 7 residues within 4Å: Chain A: L.124, L.141 Chain B: P.126, S.127, E.130, S.137 Ligands: NA.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.127, B:S.137

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.19: 4 residues within 4Å: Chain C: K.118, R.153, N.160 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:N.70, C:R.153 NAG.20: 4 residues within 4Å: Chain C: H.42, N.43, D.62, S.64 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.42, C:D.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Falconer, D.J. et al., Antibody Fucosylation Lowers the Fc gamma RIIIa/CD16a Affinity by Limiting the Conformations Sampled by the N162-Glycan. ACS Chem. Biol. (2018)

Release Date

2018-05-23

Peptides

Immunoglobulin gamma-1 heavy chain: AB
Low affinity immunoglobulin gamma Fc region receptor III-A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Immunoglobulin gamma-1 heavy chain

Low affinity immunoglobulin gamma Fc region receptor III-A