SMTL ID : 1zhn.1

Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain A: A.13, N.14, S.16, W.17 Chain B: H.34 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.17, A:N.14 Hydrogen bonds: A:S.16

1 x NAG- NAG- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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(Post Translational Modification)

NAG-NAG-MAN-MAN-MAN-FUC.2: 9 residues within 4Å: Chain A: E.107, S.108, F.122, W.123, G.124, T.125, Q.155, L.158, N.159 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.122, A:L.158 Hydrogen bonds: A:S.108, A:S.108, A:G.124

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

NAG.3: 4 residues within 4Å: Chain A: W.17, S.18, R.19, N.36 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.17, A:R.19 Hydrogen bonds: A:S.18, A:N.36

1 x PC6: 7-[(DODECANOYLOXY)METHYL]-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-3,5,8-TRIOXA-4-PHOSPHADOTRIACONTAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC6.4: 21 residues within 4Å: Chain A: C.6, Q.8, S.22, V.24, I.41, L.60, F.64, Y.67, S.70, F.71, D.74, I.92, V.112, F.114, V.120, W.127, L.144, D.147, T.150, L.157, F.165 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.24, A:I.41, A:L.60, A:F.64, A:Y.67, A:Y.67, A:Y.67, A:I.92, A:V.112, A:V.112, A:F.114, A:V.120, A:W.127, A:L.144, A:F.165 Water bridges: A:D.147, A:D.147 Salt bridges: A:D.147

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: W.25, P.233 Chain B: S.52, D.53, Y.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.52, B:D.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giabbai, B. et al., Crystal structure of mouse CD1d bound to the self ligand phosphatidylcholine: a molecular basis for NKT cell activation. J.Immunol. (2005)

Release Date

2005-07-19

Peptides

CD1d1 antigen: A
beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CD1d1 antigen

beta-2-microglobulin

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