SMTL ID : 3rzc.1

Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 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: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.23 NAG-NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, N.42, D.43 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- FUL: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-FUL.3: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 5 PLIP interactions: 5 interactions with chain A Water bridges: A:T.131 Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

1 x LGN: N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide(Non-covalent)

LGN.4: 39 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, W.63, L.66, F.70, Y.73, F.77, D.80, I.81, L.100, A.102, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, A.158, T.159, V.160, M.162, L.163, L.164, C.168, F.171 Chain C: P.30, N.32, V.52, K.69, R.96, G.97 34 PLIP interactions: 32 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.10, A:V.30, A:W.40, A:I.47, A:W.63, A:L.66, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:F.77, A:I.81, A:A.102, A:V.118, A:F.120, A:W.133, A:W.133, A:W.133, A:W.142, A:W.142, A:L.143, A:L.150, A:T.156, A:V.160, A:L.164, A:F.171 Hydrogen bonds: A:D.153, A:T.156, A:T.156, A:T.159, A:T.159, C:K.69, C:G.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, E.D. et al., Cutting Edge: Structural Basis for the Recognition of {beta}-Linked Glycolipid Antigens by Invariant NKT Cells. J.Immunol. (2011)

Release Date

2011-08-24

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha14: C
Vbeta8.2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Valpha14

Vbeta8.2

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