SMTL ID : 3ilq.1

Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 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: 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 No protein-ligand interaction detected (PLIP) 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, A:R.25 Hydrogen bonds: A:S.24, A:R.25

1 x 1O2: (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate(Non-covalent)

1O2.4: 25 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, W.40, M.69, F.70, Y.73, S.76, F.77, R.79, D.80, L.84, I.98, L.100, F.120, W.142, L.143, L.150, D.153, T.156, T.159, V.160, L.163, F.171 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.30, A:W.40, A:F.70, A:F.70, A:Y.73, A:F.77, A:L.100, A:F.120, A:F.120, A:W.142, A:L.143, A:L.150, A:T.159, A:V.160, A:F.171 Hydrogen bonds: A:S.76, A:S.76, A:R.79, A:R.79, A:T.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Lipid binding orientation within CD1d affects recognition of Borrelia burgorferi antigens by NKT cells. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-01-26

Peptides

T-cell surface glycoprotein CD1d1: A
Beta-2 microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

T-cell surface glycoprotein CD1d1

Beta-2 microglobulin

Related Entries With Identical Sequence