SMTL ID : 2q7y.2 (1 other biounit)

Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: A.19, N.20, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24, A:N.42, A:R.74

1 x IGC: N-[(1S,2R,3E)-1-({[ALPHA-D-GALACTOPYRANOSYL-(1->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL]OXY}METHYL)-2-H YDROXYHEPTADEC-3-EN-1-YL]OCTANAMIDE(Non-covalent)

IGC.4: 17 residues within 4Å: Chain A: Y.73, S.76, F.77, D.80, L.84, I.98, V.118, F.120, W.133, W.142, L.143, L.150, D.153, T.156, T.159, V.160 Ligands: PLM.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73, A:Y.73, A:F.77, A:L.84, A:I.98, A:V.118, A:F.120, A:F.120, A:W.133, A:L.143, A:L.150, A:T.156, A:T.159, A:V.160 Hydrogen bonds: A:D.80, A:T.156, A:T.156, A:T.156, A:T.156 Water bridges: A:Y.73, A:D.153

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 12 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, W.40, L.66, F.70, Y.73, L.164, C.168, F.171 Ligands: IGC.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.30, A:W.40, A:L.66, A:F.70, A:L.164, A:F.171 Hydrogen bonds: A:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zajonc, D.M. et al., Crystal Structures of Mouse CD1d-iGb3 Complex and its Cognate Valpha14 T Cell Receptor Suggest a Model for Dual Recognition of Foreign and Self Glycolipids. J.Mol.Biol. (2008)

Release Date

2008-04-01

Peptides

T-cell surface glycoprotein CD1d1: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

T-cell surface glycoprotein CD1d1

Beta-2-microglobulin

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