SMTL ID : 9fmb.1 (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- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN.1: 20 residues within 4Å: Chain A: Y.15, L.16, L.17, F.35, V.37, H.67, N.69, S.71, S.73, H.75, R.77, 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:R.77, 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: G.13, Y.15, V.37 Chain B: Y.15, L.16, L.17, T.18, T.33, F.35, V.37, E.65, H.67, N.69, S.71, H.75, N.147, D.205 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.15, B:S.73

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

NAG.3: 3 residues within 4Å: Chain A: N.211, A.212, S.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.6: 2 residues within 4Å: Chain B: W.25, N.211 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.211

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

PEG.4: 5 residues within 4Å: Chain A: L.12, V.14, Y.15, Q.103 Chain B: N.69 No protein-ligand interaction detected (PLIP)

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

ACT.5: 4 residues within 4Å: Chain A: A.20, D.23, T.31, T.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.20, A:D.23, A:T.33, A:R.77 ACT.7: 7 residues within 4Å: Chain B: L.17, T.18, P.19, A.20, D.23, T.31, T.33 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.17 Hydrogen bonds: B:A.20, B:D.23, B:T.33, B:T.33

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
A

B
B

Isoform 1 of Immunoglobulin heavy constant delta

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