SMTL ID : 3arb.1

Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylceramide analogue-OCH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

3 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: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.129

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: L.35, K.185, E.187, D.242, E.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.243 PEG.8: 7 residues within 4Å: Chain A: R.11, L.13, S.101 Chain B: F.56, S.57, K.58, W.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.11, A:S.101

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

NAG.5: 1 residues within 4Å: Chain A: N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110

1 x FEE: N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide(Non-covalent)

FEE.6: 23 residues within 4Å: Chain A: F.10, C.12, Q.14, V.30, I.47, L.66, F.70, V.72, Y.73, S.76, F.77, D.80, W.133, D.153, G.155, T.156, T.159, F.171 Chain C: P.28, N.30, D.93, R.94, G.95 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.10, A:I.47, A:L.66, A:F.70, A:Y.73, A:Y.73, A:F.77, A:F.77, A:W.133, A:T.156, A:T.159, A:F.171 Hydrogen bonds: A:D.80, A:G.155, A:T.156, A:T.156, C:N.30, C:G.95 Water bridges: C:K.67, C:K.67

1 x D12: DODECANE(Non-covalent)

D12.7: 3 residues within 4Å: Chain A: M.88, F.120, L.143 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.120, A:F.120, A:L.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wun, K.S. et al., A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells. Immunity (2011)

Release Date

2011-03-30

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18: C
NKT Vbeta8.2,NKT Vbeta8.2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18

NKT Vbeta8.2,NKT Vbeta8.2

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