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

Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.3: 8 residues within 4Å: Chain A: E.113, S.114, W.129, G.130, T.131, Q.161, L.164, N.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: W.31, D.34, L.35, P.239, E.243, T.244, W.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.243 GOL.6: 4 residues within 4Å: Chain A: Q.154 Chain C: G.98, Y.99, T.100 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.99, C:T.100, C:T.100, A:Q.154

1 x JUD: N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide(Non-covalent)

JUD.5: 30 residues within 4Å: Chain A: C.12, Q.14, V.30, I.47, M.69, F.70, Y.73, S.76, D.80, L.84, L.100, A.102, V.118, F.120, W.133, L.150, D.153, G.155, T.156, A.158, V.160, L.163, F.171 Chain B: P.30, N.32, D.53, K.69, D.95, R.96, G.97 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.14, A:V.30, A:I.47, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:L.84, A:L.100, A:V.118, A:F.120, A:W.133, A:L.150, A:V.160, A:L.163, A:F.171, A:F.171 Hydrogen bonds: A:D.80, A:D.80, A:T.156, A:T.156, B:N.32, B:G.97 Halogen bonds: B:D.53

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

NA.7: 2 residues within 4Å: Chain C: K.12, T.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.12, C:T.21 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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