SMTL ID : 2vuo.1

Crystal structure of the rabbit IgG Fc fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 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: 17 residues within 4Å: Chain A: P.4, F.13, F.15, P.16, P.17, K.18, E.30, T.32, V.36, D.37, Q.67, N.69, T.71, R.73, K.106 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN.2, NAG-NAG-BMA-MAN-NAG-GAL-MAN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.15, A:K.18, A:E.30, A:E.30, A:E.30, A:T.32 Water bridges: A:D.21, A:E.30

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN: beta-D-galactopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-MAN.2: 17 residues within 4Å: Chain B: F.13, F.15, P.16, P.17, K.18, E.30, V.31, T.32, V.34, V.36, D.37, Q.67, N.69, T.71, R.73 Ligands: NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1, NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.30, B:T.32, B:T.32 Water bridges: B:K.18, B:T.32, B:R.73, B:R.73

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: L.86, R.87, K.110, A.111, R.112, G.113, P.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.86, A:K.110, A:G.113 GOL.4: 5 residues within 4Å: Chain A: I.149, S.150, V.151, T.165, L.178 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.151 Water bridges: A:S.147, A:I.149, A:S.150, A:V.151 GOL.5: 4 residues within 4Å: Chain A: T.28, P.79, I.80, A.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.81 Water bridges: A:R.57, A:P.79 GOL.9: 5 residues within 4Å: Chain B: L.86, K.110, R.112, G.113, P.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.110, B:G.113 Water bridges: B:A.111

2 x AZI: AZIDE ION(Non-covalent)

AZI.6: 3 residues within 4Å: Chain A: E.160, D.161, N.162 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.161, A:N.162 Water bridges: A:E.160, A:E.160, A:E.160, A:E.160, A:N.162, A:N.162 AZI.10: 5 residues within 4Å: Chain A: P.126, E.128 Chain B: Y.121, T.122, K.211 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.128, A:E.128, B:T.122 Water bridges: A:R.127, B:T.122, B:T.122

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: D.21, R.27, T.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.28, A:T.28 Water bridges: A:T.28 FMT.8: 5 residues within 4Å: Chain A: K.20, S.150, E.152, S.198, M.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.20, A:S.198 Water bridges: A:S.198, A:S.198 FMT.11: 3 residues within 4Å: Chain B: I.149, S.150, V.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.151 Water bridges: B:T.165 FMT.12: 4 residues within 4Å: Chain A: K.164 Chain B: L.170, D.171, S.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.164 FMT.13: 5 residues within 4Å: Chain B: K.20, S.150, E.152, S.198, M.200 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.20, B:S.150 Water bridges: B:E.152, B:S.198, B:S.198 FMT.14: 1 residues within 4Å: Chain B: Q.114 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, E. et al., The Crystal Structure of Rabbit Igg-Fc. Biochem.J. (2009)

Release Date

2008-09-16

Peptides

IG GAMMA CHAIN C REGION: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IG GAMMA CHAIN C REGION