SMTL ID : 2po6.2 (1 other biounit)

Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 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: N.15, S.17, W.18 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: T.19, R.20, N.37, D.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.19

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

AGH.3: 33 residues within 4Å: Chain A: C.7, L.8, Q.9, A.25, W.35, V.42, W.58, L.61, F.65, Y.68, S.71, F.72, D.75, F.79, L.85, L.91, F.109, V.111, F.113, I.118, L.119, L.143, D.146, W.148, T.149, T.152, L.156, F.164 Chain C: P.28, F.29, S.30, R.94, G.95 33 PLIP interactions: 30 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Q.9, A:A.25, A:W.35, A:W.35, A:V.42, A:W.58, A:L.61, A:F.65, A:Y.68, A:Y.68, A:F.72, A:F.72, A:F.79, A:F.79, A:L.85, A:L.91, A:F.109, A:V.111, A:V.111, A:F.113, A:I.118, A:L.119, A:L.143, A:L.143, A:W.148, A:T.152, A:L.156, A:F.164 Hydrogen bonds: A:D.75, A:T.149, C:F.29, C:R.94, C:G.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borg, N.A. et al., CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor. Nature (2007)

Release Date

2007-07-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

T-cell surface glycoprotein CD1d

Beta-2-microglobulin

NKT15 alpha-chain

NKT15 beta-chain

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