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SMTL ID : 3vwk.1

Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 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, R.26, N.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.25, A:R.26

1 x 4GH: N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide(Non-covalent)

4GH.3:

25 residues within 4Å:

Chain A: C.13, L.14, Q.15, W.41, V.48, F.71, Y.74, S.77, F.78, D.81, V.82, F.85, F.115, W.132, L.149, D.152, W.154, T.155, T.158, C.167, F.170
Chain C: P.30, F.31, R.96, G.97

23 PLIP interactions:

21 interactions with chain A, 2 interactions with chain C

Hydrophobic interactions: A:Q.15, A:W.41, A:V.48, A:F.71, A:Y.74, A:Y.74, A:Y.74, A:F.78, A:V.82, A:F.85, A:F.85, A:F.115, A:W.132, A:W.132, A:L.149, A:W.154, A:T.155, A:T.158, A:F.170
Hydrogen bonds: A:D.152, A:T.155, C:R.96, 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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