SMTL ID : 3t1f.1

Crystal structure of the mouse CD1d-Glc-DAG-s2 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: W.23, S.24, N.42 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:R.74

1 x 3TF: (2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate(Non-covalent)

3TF.4: 23 residues within 4Å: Chain A: F.10, L.66, Y.73, S.76, F.77, R.79, D.80, L.84, V.85, M.88, I.96, I.98, A.102, L.116, V.118, F.120, W.133, W.142, L.143, L.150, T.156, T.159, F.171 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.10, A:L.66, A:Y.73, A:Y.73, A:F.77, A:L.84, A:V.85, A:I.96, A:L.116, A:V.118, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:T.159, A:F.171 Hydrogen bonds: A:S.76, A:S.76, A:R.79, A:R.79

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: W.31, D.34, P.239, N.240, E.243, T.244, W.245 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.34, A:N.240, A:T.244 Water bridges: A:E.243, A:E.243, A:E.243 GOL.6: 3 residues within 4Å: Chain A: H.117, Y.124 Chain B: W.60 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.60 Water bridges: B:W.60, A:Y.124 GOL.7: 2 residues within 4Å: Chain A: S.141, W.142 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain A: P.217, V.218, W.219, K.266, H.267, S.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.266, A:S.268, A:S.268 GOL.9: 4 residues within 4Å: Chain A: D.274, I.275, I.276, L.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.274, A:I.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kinjo, Y. et al., Invariant natural killer T cells recognize glycolipids from pathogenic Gram-positive bacteria. Nat.Immunol. (2011)

Release Date

2011-09-21

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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