SMTL ID : 6fgo.1 (1 other biounit)

Fc in complex with engineered calcium binding domain Z

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- MAN- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-NAG-FUC.1: 13 residues within 4Å: Chain A: F.5, F.7, K.10, T.24, V.28, D.29, Q.59, Y.60, N.61, T.63, R.65 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.60, A:R.65, A:K.10, A:K.10 Water bridges: A:Y.60, A:T.24, A:R.65 NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2: 15 residues within 4Å: Chain C: F.5, F.7, K.10, T.24, V.26, V.28, D.29, Q.59, Y.60, N.61, T.63, R.65 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1, PEG.15, PEG.17 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.60 Hydrogen bonds: C:Q.59, C:K.10 Water bridges: C:Y.60, C:T.24

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

PEG.3: 7 residues within 4Å: Chain A: E.109, P.110, Q.111, V.112, Y.113, L.196, K.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.109, A:V.112, A:Y.113, A:K.203 PEG.4: 4 residues within 4Å: Chain A: E.109, A.195, H.197 Chain B: Y.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.14 Water bridges: A:H.197 PEG.15: 4 residues within 4Å: Chain C: F.5, L.6 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.6 PEG.16: 5 residues within 4Å: Chain C: K.10, D.13, R.19, T.20, E.22 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.10, C:K.10, C:T.20, C:T.20 PEG.17: 5 residues within 4Å: Chain C: Q.59, R.65 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.2, CL.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.59

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.35, E.36, V.37, T.53, R.56, V.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.37, A:V.37, A:R.56, A:R.56 GOL.6: 1 residues within 4Å: Chain A: N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 GOL.7: 5 residues within 4Å: Chain A: K.134, D.163, D.165 Chain C: N.154, T.175 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.163, C:Q.126, C:N.154, C:T.175 Water bridges: A:D.163, A:S.167 GOL.9: 3 residues within 4Å: Chain A: S.18 Chain B: Q.9, I.35 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:S.18, A:T.20 Hydrogen bonds: B:Q.9, B:L.34 GOL.18: 7 residues within 4Å: Chain A: Q.126, N.154, T.175 Chain C: K.134, D.163, S.164, D.165 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.134, C:K.134, C:S.164, C:S.164, C:S.164, C:D.165, A:N.154 Water bridges: C:D.163 GOL.19: 4 residues within 4Å: Chain C: G.105, Q.106, R.108, Y.137 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.108 GOL.20: 2 residues within 4Å: Chain C: N.153, Y.155 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.155, C:Y.155

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain B: D.40, N.42, N.44, Y.46, D.48, E.51 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.40, B:Y.46, B:D.48, B:E.51, B:E.51 CA.21: 6 residues within 4Å: Chain D: D.40, N.42, N.44, Y.46, D.48, E.51 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.40, D:Y.46, D:D.48, D:E.51, D:E.51

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain C: S.3, V.4, K.98 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: E.109, T.201, K.203 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: Y.42, K.84 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: Q.59 Ligands: PEG.17 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: E.144, E.146, S.190 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanje, S. et al., Protein Engineering Allows for Mild Affinity-based Elution of Therapeutic Antibodies. J. Mol. Biol. (2018)

Release Date

2018-06-20

Peptides

Immunoglobulin gamma-1 heavy chain: AC
Z-Ca: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
E

D
G

Immunoglobulin gamma-1 heavy chain

Z-Ca

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