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SMTL ID : 3huj.2 (1 other biounit)

Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NDG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-BMA.1:

5 residues within 4Å:

Chain A: W.24, T.25, R.26, N.43, D.44

3 PLIP interactions:

3 interactions with chain A

Hydrophobic interactions: A:W.24
Hydrogen bonds: A:T.25, A:N.43

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

NAG.2:

4 residues within 4Å:

Chain A: A.20, N.21, S.23, W.24

4 PLIP interactions:

4 interactions with chain A

Hydrophobic interactions: A:A.20, A:W.24
Hydrogen bonds: A:S.23
Water bridges: A:S.23

1 x AGH: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE(Non-covalent)

AGH.3:

35 residues within 4Å:

Chain A: L.11, C.13, L.14, Q.15, A.31, H.39, W.41, V.48, L.67, F.71, Y.74, S.77, F.78, D.81, V.82, F.85, L.91, L.97, F.115, V.117, W.132, D.152, W.154, T.155, T.158, V.159, L.162, C.167, F.170
Chain C: P.30, F.31, S.32, D.95, R.96, G.97

36 PLIP interactions:

30 interactions with chain A, 6 interactions with chain C

Hydrophobic interactions: A:L.11, A:W.41, A:W.41, A:V.48, A:L.67, A:F.71, A:Y.74, A:Y.74, A:Y.74, A:F.78, A:V.82, A:F.85, A:L.91, A:L.97, A:F.115, A:V.117, A:W.132, A:W.132, A:W.154, A:T.155, A:T.158, A:V.159, A:L.162, A:F.170, A:F.170
Hydrogen bonds: A:T.155, C:F.31, C:R.96, C:R.96, C:R.96, C:G.97
Water bridges: A:D.152, A:D.152, A:D.152, A:K.153
Salt bridges: C:R.96

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pellicci, D.G. et al., Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors. Immunity (2009)

Release Date

2009-07-28

Peptides

T-cell surface 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
C

B
D

C
E

D
F

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

T-cell surface glycoprotein CD1d

Beta-2-microglobulin

NKT15 T cell receptor alpha-chain

NKT15 T cell receptor beta-chain

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