SMTL ID : 6miy.2 (1 other biounit)

Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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: 3 residues within 4Å: Chain A: W.23, S.24, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.2: 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 Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

1 x JTV: N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide(Non-covalent)

JTV.4: 32 residues within 4Å: Chain A: F.10, C.12, Q.14, V.30, I.47, W.63, F.70, Y.73, S.76, F.77, D.80, I.81, L.84, L.100, A.102, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, V.160, L.163, F.171 Chain B: P.30, N.32, K.69, D.95, R.96, G.97 33 PLIP interactions: 31 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.10, A:F.10, A:Q.14, A:V.30, A:I.47, A:W.63, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:L.100, A:V.118, A:V.118, A:F.120, A:W.133, A:W.133, A:L.143, A:L.150, A:V.160, A:L.163, A:F.171 Hydrogen bonds: A:D.80, A:D.80, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156, B:N.32, B:G.97

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: H.201 No protein-ligand interaction detected (PLIP) GOL.6: 7 residues within 4Å: Chain B: R.35, F.37, L.45, S.47 Chain C: Q.101, Y.102, F.103 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:F.103, B:R.35, B:S.47 Water bridges: C:Q.101, B:S.47, B:S.47

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain B: Q.7, S.8, L.22, Q.23, W.36, T.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.7, B:S.8, B:Q.23, B:T.109, B:T.109 NA.8: 6 residues within 4Å: Chain C: R.37, Q.38, D.39, H.42, G.43, R.45 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.37, C:D.39, C:R.45, C:R.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janssens, J. et al., 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies. ChemMedChem (2019)

Release Date

2019-01-09

Peptides

Antigen-presenting glycoprotein CD1d1: A
T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN: B
Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

C
H

D
F

Antigen-presenting glycoprotein CD1d1

T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN

Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN

Beta-2-microglobulin

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