SMTL ID : 3qi9.1

Crystal structure of mouse CD1d-alpha-phosphotidylinositol with mouse Valpha14-Vbeta6 2A3-D NKT TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 4 residues within 4Å: Chain A: G.130, T.131, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:S.22, A:S.22 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.24

1 x PII: 2-[(HYDROXY{[(2R,3R,5S,6R)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL]OXY}PHOSPHORYL)OXY]-1-[(PALMITOYLOXY)METHYL]ETHYL HEPTADECANOATE(Non-covalent)

PII.4: 25 residues within 4Å: Chain A: F.10, M.69, F.70, Y.73, S.76, F.77, D.80, A.102, V.118, W.133, W.142, L.143, L.150, G.155, T.156, T.159, V.160, L.163, F.171 Chain C: P.28, N.30, V.50, Q.52, K.67, R.94 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.10, A:F.10, A:F.70, A:F.70, A:Y.73, A:F.77, A:A.102, A:V.118, A:W.133, A:W.142, A:L.143, A:L.150, A:T.156, A:V.160, A:L.163, A:L.163, A:F.171 Water bridges: A:T.156, C:Q.52, C:G.95 Hydrogen bonds: C:N.30, C:Q.52, C:K.67

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: H.284 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: W.31, G.33 Chain B: S.55, F.56, S.57, Y.63 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.55, B:F.56, B:Y.63, A:G.33 GOL.7: 6 residues within 4Å: Chain D: V.154, E.155, L.156, T.171, D.172, L.189 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.154, D:L.156, D:L.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallevaey, T. et al., A molecular basis for NKT cell recognition of CD1d-self-antigen. Immunity (2011)

Release Date

2012-02-15

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
NKT TCR V alpha 14: C
NKT TCR V beta 6 2A3-D: 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 TCR V alpha 14

NKT TCR V beta 6 2A3-D

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