SMTL ID : 6mji.1

Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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- 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.2: 8 residues within 4Å: Chain C: E.113, S.114, W.129, G.130, T.131, Q.161, L.164, N.165 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.164 Hydrogen bonds: C:S.114, C:S.114, C:G.130

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

NA.3: 6 residues within 4Å: Chain A: D.161, K.162, C.163 Chain B: D.171, P.172, R.191 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.171, B:R.191, A:K.162 Water bridges: A:D.161 NA.8: 6 residues within 4Å: Chain A: L.127, L.139 Chain B: P.128, S.129, E.132, T.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.129, B:T.140, B:T.140

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.35, F.37, S.47 Chain B: Q.101, Y.102, F.103 Ligands: GOL.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.101, B:F.103, B:F.103, A:R.35 GOL.5: 9 residues within 4Å: Chain A: H.33, R.35, F.37, L.103 Chain B: Y.99, T.100, Q.101, F.103 Ligands: GOL.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.35, B:Q.101, B:Q.101 GOL.6: 6 residues within 4Å: Chain B: N.29, H.30, N.31, D.96, E.97 Chain C: K.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.29, B:N.31, B:N.31, B:E.97 GOL.7: 4 residues within 4Å: Chain B: T.87, L.110, D.151, H.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.151 GOL.9: 8 residues within 4Å: Chain C: W.31, D.34, P.239, N.240, E.243, T.244, W.245 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.34, C:N.240, C:T.244 GOL.12: 6 residues within 4Å: Chain C: W.31, P.239 Chain D: S.52, D.53, Y.63 Ligands: GOL.9 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.52, D:D.53 Water bridges: D:Y.26, C:E.243

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

NAG.10: 3 residues within 4Å: Chain C: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP)

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

JTD.11: 31 residues within 4Å: Chain A: P.30, N.32, K.69, D.95, R.96, G.97 Chain C: F.10, C.12, Q.14, S.28, V.30, W.63, M.69, F.70, Y.73, S.76, D.80, I.81, A.102, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, T.159, V.160, C.168, F.171 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.10, C:W.63, C:F.70, C:Y.73, C:Y.73, C:Y.73, C:I.81, C:A.102, C:V.118, C:V.118, C:F.120, C:F.120, C:W.133, C:L.143, C:L.150, C:T.159, C:V.160, C:F.171 Hydrogen bonds: C:D.80, C:T.156, C:T.156, A:N.32, A:G.97 Water bridges: 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 joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN: 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 joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN

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

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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