SMTL ID : 3quy.1

Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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(Post Translational Modification)

NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130 Water bridges: A:T.131

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

NAG.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.19 Hydrogen bonds: A:S.22 NAG.3: 3 residues within 4Å: Chain A: W.23, S.24, N.42 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24, A:T.26, A:R.74, A:R.74

1 x QUY: (2S,3R,4S,5R,6S)-6-[(2S,3S,4R)-2-(hexacosanoylamino)-3,4-dihydroxy-octadecoxy]-3,4,5-trihydroxy-N-(phenylmethyl)oxane-2-carboxamide(Non-covalent)

QUY.4: 33 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, L.66, H.68, M.69, F.70, Y.73, S.76, F.77, D.80, I.81, L.100, A.102, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163, C.168, F.171 Chain C: P.30, N.32, R.96, G.97 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.10, A:V.30, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:I.81, A:L.100, A:A.102, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:T.156, A:V.160, A:F.171, A:F.171 Hydrogen bonds: A:D.80, A:D.153, A:G.155, A:T.156, A:T.156, A:T.159, C:N.32, C:R.96, C:G.97 Water bridges: A:D.153, A:T.156, A:T.159

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain D: G.98, Y.99, T.100 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.100, D:T.100 Water bridges: D:D.96, D:G.98, D:G.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aspeslagh, S. et al., Galactose-modified iNKT cell agonists stabilized by an induced fit of CD1d prevent tumour metastasis. Embo J. (2011)

Release Date

2011-06-29

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2 microglobulin: B
Valpha14 (mouse variable domain, human constant domain): C
Vbeta8.2 (mouse variable domain, human constant domain): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2 microglobulin

Valpha14 (mouse variable domain, human constant domain)

Vbeta8.2 (mouse variable domain, human constant domain)

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