SMTL ID : 9fmb.2 (1 other biounit)

Crystal structure of human IgD-Fc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.1: 18 residues within 4Å: Chain A: Y.15, L.16, L.17, F.35, V.37, H.67, N.69, S.71, S.73, L.105 Chain B: P.11, G.13, Y.15, V.37 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.15, A:S.73

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN-MAN.2: 20 residues within 4Å: Chain A: P.11, G.13, Y.15, V.37 Chain B: Y.15, L.16, L.17, T.18, T.33, F.35, H.67, N.69, S.71, H.75, R.77, L.105, N.147 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.15

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

EDO.3: 3 residues within 4Å: Chain A: Q.114, V.117, T.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.114, A:G.142 EDO.4: 3 residues within 4Å: Chain A: H.45, T.47, N.96 No protein-ligand interaction detected (PLIP)

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain A: V.50, P.55, T.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.50 Hydrogen bonds: A:T.56 ACT.6: 4 residues within 4Å: Chain A: L.17, T.31, F.32, T.33 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.17 Hydrogen bonds: A:D.23, A:D.23, A:T.33 ACT.8: 2 residues within 4Å: Chain B: A.51, K.53 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.53

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

NAG.7: 2 residues within 4Å: Chain B: W.25, N.211 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, A.M. et al., The Crystal Structure of Human IgD-Fc Reveals Unexpected Differences With Other Antibody Isotypes. Proteins (2024)

Release Date

2024-12-04

Peptides

Isoform 1 of Immunoglobulin heavy constant delta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isoform 1 of Immunoglobulin heavy constant delta

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