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SMTL ID : 3vwj.1

Ternary crystal structure of the human NKT TCR-CD1d-C20:2 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1:	3 residues within 4Å: Chain A: A.20, N.21, W.24 No protein-ligand interaction detected (PLIP)
NAG.2:	4 residues within 4Å: Chain A: W.24, T.25, N.43, D.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.25

1 x DB3: (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide(Non-covalent)

DB3.3:

29 residues within 4Å:

Chain A: C.13, L.14, Q.15, G.29, L.30, A.31, H.39, F.71, Y.74, S.77, F.78, D.81, F.85, L.91, L.97, F.115, V.117, W.132, L.149, D.152, W.154, T.155, V.159, L.162
Chain C: P.30, F.31, S.32, R.96, G.97

27 PLIP interactions:

24 interactions with chain A, 3 interactions with chain C

Hydrophobic interactions: A:Q.15, A:A.31, A:F.71, A:Y.74, A:Y.74, A:Y.74, A:Y.74, A:F.78, A:F.85, A:F.85, A:L.91, A:L.97, A:F.115, A:F.115, A:V.117, A:W.132, A:L.149, A:T.155, A:V.159, A:L.162
Hydrogen bonds: A:S.77, A:D.152, A:T.155, A:T.155, C:S.32, C:S.32, C:G.97

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

2 residues within 4Å:

Chain D: G.29, D.31

1 PLIP interactions:

1 interactions with chain D

Metal complexes: D:D.31

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wun, K.S. et al., Human and mouse type I natural killer T cell antigen receptors exhibit different fine specificities for CD1d-antigen complex. J.Biol.Chem. (2012)

Release Date

2012-10-03

Peptides

Antigen-presenting glycoprotein CD1d: A
Beta-2-microglobulin: B
NKT15 T cell receptor alpha-chain: C
NKT15 T cell receptor beta-chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

NKT15 T cell receptor alpha-chain

NKT15 T cell receptor beta-chain

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