SMTL ID : 6mj4.1

Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.4: 7 residues within 4Å: Chain A: R.35, F.37, S.47 Chain B: Q.101, Y.102, F.103 Ligands: GOL.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.101, B:F.103, B:F.103 Water bridges: A:R.35 GOL.5: 5 residues within 4Å: Chain A: K.135, S.136, W.180, S.181 Chain B: L.144 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.136, A:S.136, A:W.180, B:T.146 Water bridges: A:S.181 GOL.6: 5 residues within 4Å: Chain A: Q.39, T.41, G.42, T.88 Chain B: Q.38 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.38, A:D.40, A:G.42, A:T.88 GOL.8: 8 residues within 4Å: Chain C: E.97, Q.99, Q.121, G.122 Chain D: H.31, P.32, W.60, F.62 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.99, D:W.60 Water bridges: C:G.122 GOL.9: 4 residues within 4Å: Chain C: W.31 Chain D: S.52, Y.63, L.65 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.52, C:A.241 Water bridges: D:Y.63

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

NA.7: 5 residues within 4Å: Chain A: L.127 Chain B: P.128, S.129, E.132, T.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.129, B:E.132, B:T.140

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

NAG.10: 4 residues within 4Å: Chain C: A.19, N.20, S.22, W.23 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.20

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

JTG.11: 35 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, L.66, M.69, F.70, Y.73, S.76, D.80, I.81, L.84, L.100, A.102, F.120, W.133, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163, C.168, F.171 32 PLIP interactions: 30 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.10, C:I.47, C:W.63, C:L.66, C:F.70, C:F.70, C:Y.73, C:Y.73, C:Y.73, C:I.81, C:L.84, C:L.100, C:F.120, C:F.120, C:W.133, C:W.133, C:L.143, C:L.150, C:T.159, C:V.160, C:L.163, C:F.171 Hydrogen bonds: C:D.80, C:D.153, C:D.153, C:G.155, C:T.156, C:T.156, A:N.32, A:G.97 Water bridges: C:Q.154, 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,T cell 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,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Related Entries With Identical Sequence