SMTL ID : 3agv.1

Crystal structure of a human IgG-aptamer complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

1 x MAN- MAN- NDG- GLA: alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose

MAN-MAN-NDG-GLA.1: 11 residues within 4Å: Chain A: F.5, F.7, P.8, P.9, K.10, D.13, E.22, V.23, T.24, V.26 Ligands: NDG-NAG-BMA-MAN-NAG-GAL-MAN-FUL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.10, A:D.13, A:E.22, A:E.22, A:T.24, A:K.10

1 x NDG- NAG- BMA- MAN- NAG- GAL- MAN- FUL: 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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-NAG-BMA-MAN-NAG-GAL-MAN-FUL.2: 18 residues within 4Å: Chain B: F.5, F.7, P.8, P.9, K.10, E.22, V.23, T.24, V.26, V.28, D.29, Q.59, Y.60, N.61, T.63, R.65 Ligands: MAN-MAN-NDG-GLA.1, MAN-MAN-NDG-GLA.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.29, B:N.61, B:T.63, B:T.63, B:Q.59, B:N.61, B:K.10, B:E.22, B:T.24, B:K.10, B:T.24 Water bridges: B:K.10

2 x CA: CALCIUM ION(Non-functional Binders)

CA.3: 1 residues within 4Å: Chain C: G.7 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain D: G.7, G.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomura, Y. et al., Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex. Nucleic Acids Res. (2010)

Release Date

2010-11-10

Peptides

Ig gamma-1 chain C region: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ig gamma-1 chain C region