SMTL ID : 5hvw.1 (1 other biounit)

Monomeric IgG4 Fc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

6 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: 15 residues within 4Å: Chain A: F.7, F.9, P.10, P.11, K.12, E.24, T.26, V.30, D.31, Q.61, F.62, N.63, T.65, R.67, K.100 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.62 Hydrogen bonds: A:Q.61, A:F.9, A:K.12, A:E.24, A:E.24, A:T.26, A:T.26 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.5: 15 residues within 4Å: Chain B: F.7, F.9, P.10, P.11, K.12, E.24, T.26, V.30, D.31, Q.61, F.62, N.63, T.65, R.67, K.100 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.62 Hydrogen bonds: B:Q.61, B:F.9, B:K.12, B:E.24, B:E.24, B:T.26, B:T.26 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.9: 15 residues within 4Å: Chain C: F.7, F.9, P.10, P.11, K.12, E.24, T.26, V.30, D.31, Q.61, F.62, N.63, T.65, R.67, K.100 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.62 Hydrogen bonds: C:Q.61, C:F.9, C:K.12, C:E.24, C:E.24, C:T.26, C:T.26 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.13: 15 residues within 4Å: Chain D: F.7, F.9, P.10, P.11, K.12, E.24, T.26, V.30, D.31, Q.61, F.62, N.63, T.65, R.67, K.100 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.62 Hydrogen bonds: D:Q.61, D:F.9, D:K.12, D:E.24, D:T.26 Water bridges: D:T.26 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.17: 15 residues within 4Å: Chain E: F.7, F.9, P.10, P.11, K.12, E.24, T.26, V.30, D.31, Q.61, F.62, N.63, T.65, R.67, K.100 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.62 Hydrogen bonds: E:Q.61, E:F.9, E:K.12, E:E.24, E:T.26 Water bridges: E:T.26 NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG-FUC.21: 15 residues within 4Å: Chain F: F.7, F.9, P.10, P.11, K.12, E.24, T.26, V.30, D.31, Q.61, F.62, N.63, T.65, R.67, K.100 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.62 Hydrogen bonds: F:Q.61, F:F.9, F:K.12, F:E.24, F:T.26 Water bridges: F:T.26

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: ZN.6, ZN.10 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:H.51, B:H.51, A:H.51, H2O.3, H2O.6, H2O.9 ZN.3: 3 residues within 4Å: Chain A: H.199, H.201 Chain D: H.76 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.199, A:H.201, D:H.76, H2O.3 ZN.6: 5 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: ZN.2, ZN.10 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:H.51, B:H.51, A:H.51, H2O.3, H2O.6, H2O.9 ZN.7: 3 residues within 4Å: Chain B: H.199, H.201 Chain F: H.76 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.199, B:H.201, F:H.76, H2O.6 ZN.10: 5 residues within 4Å: Chain A: H.51 Chain B: H.51 Chain C: H.51 Ligands: ZN.2, ZN.6 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:H.51, B:H.51, A:H.51, H2O.3, H2O.6, H2O.9 ZN.11: 3 residues within 4Å: Chain C: H.199, H.201 Chain E: H.76 4 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:H.76, C:H.199, C:H.201, H2O.9 ZN.14: 5 residues within 4Å: Chain D: H.51 Chain E: H.51 Chain F: H.51 Ligands: ZN.18, ZN.22 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:H.51, D:H.51, F:H.51, H2O.12, H2O.15, H2O.18 ZN.15: 3 residues within 4Å: Chain A: H.76 Chain D: H.199, H.201 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.76, D:H.199, D:H.201, H2O.13 ZN.18: 5 residues within 4Å: Chain D: H.51 Chain E: H.51 Chain F: H.51 Ligands: ZN.14, ZN.22 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:H.51, D:H.51, F:H.51, H2O.12, H2O.15, H2O.18 ZN.19: 3 residues within 4Å: Chain C: H.76 Chain E: H.199, H.201 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:H.199, E:H.201, C:H.76, H2O.16 ZN.22: 5 residues within 4Å: Chain D: H.51 Chain E: H.51 Chain F: H.51 Ligands: ZN.14, ZN.18 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: E:H.51, F:H.51, D:H.51, H2O.12, H2O.15, H2O.18 ZN.23: 3 residues within 4Å: Chain B: H.76 Chain F: H.199, H.201 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:H.76, F:H.199, F:H.201, H2O.19

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: I.143, A.144, V.145, T.159, T.160, P.162, L.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.145, A:V.145 GOL.8: 7 residues within 4Å: Chain B: I.143, A.144, V.145, T.159, T.160, P.162, L.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.145, B:V.145 GOL.12: 7 residues within 4Å: Chain C: I.143, A.144, V.145, T.159, T.160, P.162, L.172 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.145, C:V.145 GOL.16: 7 residues within 4Å: Chain D: I.143, A.144, V.145, T.159, T.160, P.162, L.172 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.145, D:V.145 GOL.20: 7 residues within 4Å: Chain E: I.143, A.144, V.145, T.159, T.160, P.162, L.172 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.145, E:V.145 GOL.24: 7 residues within 4Å: Chain F: I.143, A.144, V.145, T.159, T.160, P.162, L.172 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.145, F:V.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shan, L. et al., Generation and Characterization of an IgG4 Monomeric Fc Platform. Plos One (2016)

Release Date

2016-08-17

Peptides

Ig gamma-4 chain C region: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Ig gamma-4 chain C region

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