SMTL ID : 6omg.1

Structure of mouse CD1D- Glc-DAG (sn-1 C18:0, sn-2 C18:1c9)-iNKT TCR Ternary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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: 4 residues within 4Å: Chain C: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 8 residues within 4Å: Chain C: 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

4 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.103 Water bridges: B:F.103 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 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.33, A:R.35, B:Y.99, B:Q.101 GOL.8: 6 residues within 4Å: Chain C: C.12, Q.14, S.28, F.70, Y.73 Ligands: MVV.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.28 GOL.9: 4 residues within 4Å: Chain C: H.117, Y.124 Chain D: K.58, W.60 6 PLIP interactions: 6 interactions with chain C Water bridges: C:S.101, C:S.101, C:S.101, C:S.101, C:H.117, C:Y.124

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

NA.6: 6 residues within 4Å: Chain A: Q.7, S.8, L.22, Q.23, W.36, T.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.7, A:S.8, A:S.8, A:Q.23 NA.7: 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:G.43, B:R.45, B:R.45 NA.11: 5 residues within 4Å: Chain A: R.96, L.100 Chain C: R.79, D.80, E.83 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.96, C:R.79, C:R.79, C:D.80 NA.12: 5 residues within 4Å: Chain C: P.52, W.53, S.54, Q.55 Ligands: NA.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.53, C:Q.55 NA.13: 3 residues within 4Å: Chain C: W.53, G.56 Ligands: NA.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.56

1 x MVV: (2R)-1-(alpha-D-glucopyranosyloxy)-3-(octadecanoyloxy)propan-2-yl (9Z)-octadec-9-enoate(Non-covalent)

MVV.10: 28 residues within 4Å: Chain A: P.30, N.32, D.95, R.96, G.97 Chain C: C.12, L.66, Y.73, S.76, F.77, D.80, L.84, V.85, E.92, A.102, V.118, F.120, V.126, W.133, W.142, L.150, D.153, G.155, T.156, T.159, L.163, C.168 Ligands: GOL.8 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.66, C:Y.73, C:Y.73, C:F.77, C:L.84, C:V.85, C:E.92, C:A.102, C:V.118, C:F.120, C:F.120, C:V.126, C:W.133, C:L.150, C:T.159, C:L.163, C:L.163 Hydrogen bonds: C:D.153, C:G.155, C:T.156, C:T.156, A:N.32, A:G.97 Water bridges: C:D.153, C:D.153, C:T.159, C:T.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dirk, M.Z. et al., Structure of mouse CD1D- Glc-DAG (sn-1 C18:0, sn-2 C18:1c9)-iNKT TCR Ternary complex. To Be Published

Release Date

2020-04-22

Peptides

CHIMERIC T CELL ANTIGEN RECEPTOR ALPHA CHAIN VA14,VA24: A
CHIMERIC T CELL ANTIGEN RECEPTOR BETA CHAIN VB8.2, VB11: 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

CHIMERIC T CELL ANTIGEN RECEPTOR ALPHA CHAIN VA14,VA24

CHIMERIC T CELL ANTIGEN RECEPTOR BETA CHAIN VB8.2, VB11

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

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