SMTL ID : 4en3.1

Crystal structure of a human Valpha24(-) NKT TCR in complex with CD1d/alpha-galactosylceramide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 5 residues within 4Å: Chain A: W.24, T.25, R.26, N.43 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.24 Hydrogen bonds: A:N.43 NAG.2: 1 residues within 4Å: Ligands: NAG.1 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: A.20, N.21, S.23, W.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.21, A:N.21 NAG.6: 6 residues within 4Å: Chain B: A.190, N.194, I.198, P.199, F.204 Ligands: FUC.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.194, B:P.199 NAG.8: 2 residues within 4Å: Chain C: V.55, N.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.56

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

AGH.4: 33 residues within 4Å: Chain A: C.13, L.14, Q.15, L.30, A.31, H.39, W.41, V.48, W.64, L.67, F.71, V.73, Y.74, S.77, F.78, D.81, F.85, L.97, F.115, W.132, W.141, L.149, D.152, W.154, T.155, T.158, L.162, F.170 Chain B: S.31, N.33, D.96, R.97, G.98 34 PLIP interactions: 26 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Q.15, A:W.41, A:W.41, A:V.48, A:W.64, A:L.67, A:F.71, A:F.71, A:Y.74, A:F.78, A:F.78, A:F.85, A:F.115, A:W.132, A:W.141, A:L.149, A:W.154, A:T.155, A:T.158, A:L.162, A:F.170, A:F.170 Hydrogen bonds: A:T.155, A:T.155, B:S.31, B:N.33, B:R.97, B:R.97, B:G.98 Water bridges: A:D.152, A:D.152, B:I.32, B:N.33 Salt bridges: B:R.97

1 x FUC: alpha-L-fucopyranose(Non-functional Binders)

FUC.5: 1 residues within 4Å: Ligands: NAG.6 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: E.84 Chain B: L.101, G.102, R.103 Chain C: K.34, Y.36, Y.51, Y.53 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.34, C:K.34, C:Y.53, C:Y.53, B:R.103 Water bridges: B:L.104 GOL.9: 8 residues within 4Å: Chain B: L.104, Y.105, F.106 Chain C: Y.38, L.46, H.47, L.48, D.62 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.62, B:F.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Sagaseta, J. et al., The Molecular Basis for Recognition of CD1d/alpha-Galactosylceramide by a Human Non-Valpha24 T Cell Receptor Struct. Title. Plos Biol. (2012)

Release Date

2012-10-31

Peptides

Antigen-presenting glycoprotein CD1d: A
HUMAN NKT TCR ALPHA CHAIN: B
HUMAN NKT TCR BETA CHAIN: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

Antigen-presenting glycoprotein CD1d

HUMAN NKT TCR ALPHA CHAIN

HUMAN NKT TCR BETA CHAIN

Beta-2-microglobulin