SMTL ID : 6mss.1

Diversity in the type II Natural Killer T cell receptor repertoire and antigen specificity leads to differing CD1d docking strategies

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: A.19, N.20, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:R.25, A:N.42

1 x SRV: (2S)-2-(heptadecanoyloxy)-3-{[(10S)-10-methyloctadecanoyl]oxy}propyl alpha-D-glucopyranosiduronic acid(Non-covalent)

SRV.4: 31 residues within 4Å: Chain A: F.10, V.30, W.63, L.66, H.68, M.69, F.70, V.72, Y.73, S.76, F.77, D.80, I.81, M.88, E.92, A.102, L.116, V.118, F.120, V.126, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163, F.171 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.10, A:V.30, A:W.63, A:L.66, A:F.70, A:F.70, A:F.77, A:F.77, A:I.81, A:E.92, A:A.102, A:L.116, A:V.118, A:V.118, A:F.120, A:V.126, A:W.133, A:W.133, A:W.142, A:L.143, A:L.150, A:L.150, A:V.160, A:L.163, A:F.171, A:F.171 Hydrogen bonds: A:S.76, A:G.155, A:T.156, A:T.159 Salt bridges: A:H.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Almeida, C.F. et al., Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors. Nat Commun (2019)

Release Date

2019-10-02

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
A11B8.2 NKT TCR alpha-chain: C
A11B8.2 NKT TCR beta-chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

A11B8.2 NKT TCR alpha-chain

A11B8.2 NKT TCR beta-chain

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