SMTL ID : 6miv.1

Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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: 3 residues within 4Å: Chain C: W.23, S.24, N.42 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 C: 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 C Hydrophobic interactions: C:F.128, C:L.164 Hydrogen bonds: C:S.114, C:S.114, C:G.130

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

NA.3: 5 residues within 4Å: Chain A: D.121, A.123, Y.125, D.142 Chain B: T.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.121, A:Y.125 NA.5: 6 residues within 4Å: Chain B: R.37, Q.38, D.39, H.42, G.43, R.45 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.39, B:D.39, B:D.39, B:R.45, B:R.45 NA.7: 4 residues within 4Å: Chain B: K.12, V.13, A.14, D.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.219 Water bridges: B:S.216

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.35, F.37, S.47 Chain B: T.100, Q.101, Y.102, F.103 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.35, A:S.47, B:F.103 GOL.6: 4 residues within 4Å: Chain A: G.97 Chain B: G.98, Y.99, T.100 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.99, B:T.100, B:T.100, A:G.97 Water bridges: B:D.96, B:G.98 GOL.10: 5 residues within 4Å: Chain C: P.217, V.218, W.219, K.266, H.267 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.218 Water bridges: C:S.268 GOL.11: 7 residues within 4Å: Chain C: D.34, Y.214, P.239, N.240, E.243, T.244, W.245 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.240, C:T.244, C:W.245 Water bridges: C:E.243

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 4 residues within 4Å: Chain C: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

1 x JU1: N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide(Non-covalent)

JU1.9: 34 residues within 4Å: Chain A: P.30, N.32, D.53, K.69, D.95, R.96, G.97 Chain C: F.10, C.12, Q.14, S.28, V.30, I.47, W.63, L.66, F.70, Y.73, S.76, F.77, D.80, I.81, L.100, A.102, F.120, W.133, W.142, L.150, D.153, Q.154, G.155, T.156, V.160, C.168, F.171 29 PLIP interactions: 27 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.10, C:F.10, C:Q.14, C:V.30, C:I.47, C:W.63, C:L.66, C:F.70, C:F.70, C:F.70, C:Y.73, C:Y.73, C:Y.73, C:F.77, C:I.81, C:L.100, C:F.120, C:W.142, C:L.150, C:V.160, C:F.171 Hydrogen bonds: C:D.80, C:G.155, C:T.156, C:T.156, A:N.32, A:G.97 Water bridges: C:D.153, C:Q.154

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

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,Human nkt tcr alpha chain: A
Beta-chain,Tcell receptor chain,T cell receptor beta constant 2: B
Antigen-presenting glycoprotein CD1d1: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

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,Human nkt tcr alpha chain

Beta-chain,Tcell receptor chain,T cell receptor beta constant 2

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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