SMTL ID : 3rtq.1

Structure of the mouse CD1d-HS44-iNKT TCR complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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.23, S.24, R.25, N.42, V.75 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.75

1 x NAG- NAG- BMA- FUL: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-FUL.2: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130

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

NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP)

1 x H4S: N-[(2S,3S,4R)-3,4-dihydroxy-1-{[(1S,2S,3R,4R,5S)-2,3,4,5-tetrahydroxycyclohexyl]amino}octadecan-2-yl]hexacosanamide(Non-covalent)

H4S.4: 35 residues within 4Å: Chain A: F.10, C.12, Q.14, S.28, V.30, W.40, I.47, L.66, M.69, F.70, Y.73, S.76, F.77, D.80, I.81, L.84, L.100, A.102, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, V.160, L.163, C.168, F.171 Chain C: P.30, N.32, R.96, G.97 34 PLIP interactions: 30 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.10, A:Q.14, A:V.30, A:W.40, A:I.47, A:L.66, A:F.70, A:F.70, A:Y.73, A:Y.73, A:F.77, A:I.81, A:L.84, A:L.100, A:V.118, A:V.118, A:F.120, A:W.133, A:W.142, A:L.143, A:T.156, A:F.171, C:P.30 Hydrogen bonds: A:D.80, A:D.153, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156, A:T.159, C:N.32, C:R.96, C:G.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerzerho, J. et al., Structural and functional characterization of a novel nonglycosidic type I NKT agonist with immunomodulatory properties. J.Immunol. (2012)

Release Date

2012-02-22

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha14 (mouse variable domain, human constant domain): C
V beta8.2 (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)

V beta8.2 (mouse variable domain, human constant domain)

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