SMTL ID : 4zak.1

Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-1-1-1-1-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: 4 residues within 4Å: Chain A: 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: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24, A:N.42, A:R.74

1 x 4LX: N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide(Non-covalent)

4LX.4: 32 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, W.63, F.70, Y.73, S.76, D.80, I.81, L.100, A.102, G.103, V.118, W.133, W.142, L.150, D.153, G.155, T.156, V.160, L.163, L.164, C.168, F.171 Chain C: P.30, N.32, D.95, R.96, G.97 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:W.40, A:W.63, A:F.70, A:F.70, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:I.81, A:L.100, A:V.118, A:W.142, A:L.150, A:T.156, A:L.163, A:L.164, A:F.171 Hydrogen bonds: A:G.155, A:T.156, A:T.156, A:T.156, A:T.156, C:N.32, C:R.96, C:G.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birkholz, A.M. et al., A Novel Glycolipid Antigen for NKT Cells That Preferentially Induces IFN-gamma Production. J Immunol. (2015)

Release Date

2015-07-01

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain: C
T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain

T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region

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