SMTL ID : 6mjj.1

Crystal structure of the mCD1d/xxm (JJ290) /iNKTCR ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 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 Water bridges: C:T.131 Hydrophobic interactions: C:F.128, C:L.164 Hydrogen bonds: C:S.114, C:S.114, C:G.130

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.35, F.37, S.47 Chain B: Q.101, Y.102, F.103 Ligands: GOL.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.35, A:R.35, A:S.47, B:F.103 Water bridges: A:R.35, B:F.103 GOL.4: 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.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.99, B:Q.101, A:H.33, A:R.35 GOL.5: 6 residues within 4Å: Chain A: Q.39, D.40, T.41, G.42, T.88 Chain B: Q.38 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.38, A:Q.39, A:G.42, A:T.88, A:T.88 Water bridges: A:Q.39 GOL.6: 6 residues within 4Å: Chain A: K.135, S.136, W.180 Chain B: F.126, L.144, T.146 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.136, A:S.136, B:T.146 Water bridges: A:S.181 GOL.11: 7 residues within 4Å: Chain A: T.3, F.105 Chain B: H.42, G.43, L.44, R.45 Ligands: NA.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.3, A:F.105, B:G.43 Water bridges: A:F.105 GOL.13: 4 residues within 4Å: Chain A: G.97 Chain B: G.98, Y.99, T.100 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.99, B:T.100, A:G.97 Water bridges: B:D.96, B:D.96, B:D.96, B:G.98, B:T.100, B:Y.102 GOL.17: 3 residues within 4Å: Chain C: F.49, Q.55, N.60 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.47, C:Q.55, C:N.60 Water bridges: C:F.49 GOL.21: 5 residues within 4Å: Chain C: L.13, S.101, H.117 Chain D: K.58, W.60 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.101, C:H.117, D:W.60 Water bridges: C:R.11 GOL.22: 6 residues within 4Å: Chain C: W.31, P.239, N.240 Chain D: S.52, Y.63, L.65 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.52 Water bridges: C:Q.36, C:Q.36 GOL.23: 9 residues within 4Å: Chain C: E.97, Q.99, Q.121, G.122 Chain D: H.31, P.32, W.60, S.61, F.62 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Water bridges: C:G.122, D:H.31, D:D.59, D:D.59

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

NA.7: 5 residues within 4Å: Chain A: L.100, G.101, R.102 Chain B: Y.51 Chain C: E.83 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:R.79 Hydrogen bonds: A:G.101 NA.8: 7 residues within 4Å: Chain A: T.3, V.5, F.105, G.106, A.107 Chain B: G.43 Ligands: GOL.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.5, B:G.43 Water bridges: A:A.107 NA.9: 3 residues within 4Å: Chain A: L.12, C.20, V.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.21, A:V.21 NA.10: 3 residues within 4Å: Chain A: S.47, L.48, T.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.47 NA.12: 6 residues within 4Å: Chain A: G.97 Chain B: Y.99 Chain C: A.152, D.153, Q.154 Ligands: NA.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.152, C:Q.154 NA.14: 6 residues within 4Å: Chain A: A.99 Chain B: N.32, Y.34, G.95, D.96, G.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.32, B:Y.34, B:D.96 Water bridges: B:D.96, B:Q.101 NA.15: 3 residues within 4Å: Chain B: K.19, K.66, E.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.19, B:K.66 NA.16: 3 residues within 4Å: Chain A: Q.126 Chain B: S.129, A.131 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.129, A:Q.126, A:Q.126 NA.20: 7 residues within 4Å: Chain A: N.32, G.97 Chain C: D.153, Q.154, G.155 Ligands: NA.12, JU4.19 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.32, A:N.32, C:D.153, C:Q.154, C:G.155

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

NAG.18: 3 residues within 4Å: Chain C: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP)

1 x JU4: N-[(2S,3S,4R)-1-({4-O-[(3,4-dichlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide(Non-covalent)

JU4.19: 34 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, I.47, W.63, M.69, F.70, Y.73, S.76, D.80, I.81, L.100, A.102, F.120, W.133, W.142, L.150, D.153, G.155, T.156, T.159, V.160, L.163, C.168, F.171 Ligands: NA.20 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.10, C:Q.14, C:V.30, C:I.47, C:W.63, C:F.70, C:F.70, C:Y.73, C:Y.73, C:Y.73, C:I.81, C:L.100, C:F.120, C:W.133, C:W.142, C:L.150, C:T.159, C:V.160, C:L.163, C:F.171 Hydrogen bonds: C:D.80, C:D.153, C:G.155, C:T.156, C:T.156, A:N.32, A:G.97 Water bridges: C:T.156

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

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

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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