SMTL ID : 2akr.3 (3 other biounits)

Structural basis of sulfatide presentation by mouse CD1d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-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: 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:T.131

5 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:S.22 Water bridges: A:N.20, A:S.22 NAG.3: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24, A:T.26, A:R.74 NAG.5: 4 residues within 4Å: Chain C: A.19, N.20, S.22, W.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.22 NAG.6: 3 residues within 4Å: Chain C: W.23, S.24, N.42 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.23 Hydrogen bonds: C:S.24, C:N.42 Water bridges: C:T.26, C:R.74, C:R.74, C:R.74 NAG.7: 4 residues within 4Å: Chain C: G.130, T.131, Q.161, N.165 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.161 Hydrogen bonds: C:Q.161, C:Q.161, C:N.165 Water bridges: C:T.131

2 x CIS: (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE(Non-covalent)

CIS.4: 26 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, I.47, L.66, F.70, Y.73, S.76, R.79, D.80, L.84, I.98, L.100, V.118, F.120, W.133, W.142, L.143, D.153, G.155, T.156, T.159, V.160 Chain C: K.86, K.91 31 PLIP interactions: 27 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:V.30, A:I.47, A:L.66, A:F.70, A:Y.73, A:Y.73, A:I.98, A:I.98, A:L.100, A:F.120, A:F.120, A:W.133, A:W.142, A:L.143, A:T.159, A:V.160 Hydrogen bonds: A:R.79, A:R.79, A:D.80, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156, C:K.86 Water bridges: A:Y.73, A:S.76, C:K.91 Salt bridges: A:R.79, C:K.91, C:K.91 CIS.8: 30 residues within 4Å: Chain C: F.10, C.12, S.28, V.30, I.47, L.66, F.70, Y.73, S.76, F.77, R.79, D.80, I.81, V.85, L.100, L.116, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163, C.168, F.171 35 PLIP interactions: 35 interactions with chain C Hydrophobic interactions: C:F.10, C:F.10, C:V.30, C:I.47, C:L.66, C:F.70, C:Y.73, C:Y.73, C:Y.73, C:F.77, C:F.77, C:I.81, C:V.85, C:L.116, C:V.118, C:V.118, C:F.120, C:W.133, C:W.133, C:W.142, C:L.143, C:L.150, C:T.159, C:V.160, C:F.171 Hydrogen bonds: C:R.79, C:D.80, C:T.156, C:T.156, C:T.156 Water bridges: C:Y.73, C:G.155, C:G.155, C:G.155, C:T.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zajonc, D.M. et al., Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity. J.Exp.Med. (2005)

Release Date

2005-12-06

Peptides

T-cell surface glycoprotein CD1d1: AC
Beta-2-microglobulin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

B
D

D
B

T-cell surface glycoprotein CD1d1

Beta-2-microglobulin

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