SMTL ID : 6bmh.1 (3 other biounits)

Crystal structure of MHC-I like protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-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: 4 residues within 4Å: Chain A: G.127, T.128, Q.158, N.162 No protein-ligand interaction detected (PLIP)

1 x F61: N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide(Non-covalent)

F61.2: 20 residues within 4Å: Chain A: C.9, M.66, V.69, Y.70, S.73, F.74, D.77, L.97, T.99, V.115, V.123, W.130, P.143, L.147, D.150, G.152, T.153, T.156, V.157, L.160 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.70, A:Y.70, A:Y.70, A:F.74, A:L.97, A:T.99, A:V.115, A:V.115, A:V.123, A:W.130, A:W.130, A:P.143, A:L.147, A:T.153, A:T.156, A:V.157, A:L.160 Hydrogen bonds: A:D.77, A:T.153, A:T.153 Water bridges: A:T.153, A:T.153

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

NAG.3: 5 residues within 4Å: Chain A: W.20, S.21, R.22, N.39, R.71 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.20, A:R.22 Hydrogen bonds: A:S.21, A:N.39, A:R.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sundararaj, S. et al., Differing roles of CD1d2 and CD1d1 proteins in type I natural killer T cell development and function. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-01-31

Peptides

Antigen-presenting glycoprotein CD1d2: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antigen-presenting glycoprotein CD1d2

Beta-2-microglobulin

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