SMTL ID : 4mng.1 (1 other biounit)

Structure of the DP10.7 TCR with CD1d-sulfatide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain B: A.20, N.21, W.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.21 NAG.2: 5 residues within 4Å: Chain B: W.24, T.25, R.26, N.43, D.44 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.24, B:R.26 Hydrogen bonds: B:T.25, B:N.43, B:D.44 NAG.3: 2 residues within 4Å: Chain B: S.111, N.164 No protein-ligand interaction detected (PLIP)

1 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: 33 residues within 4Å: Chain B: C.13, L.14, Q.15, L.30, A.31, W.41, V.48, W.64, F.71, Y.74, S.77, F.78, R.80, D.81, V.82, L.91, V.117, L.125, W.132, W.141, L.149, D.152, W.154, T.155, T.158, L.162, T.166, C.167, F.170 Chain C: W.99, G.100, F.101, P.102 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.15, B:A.31, B:W.41, B:V.48, B:W.64, B:F.71, B:Y.74, B:Y.74, B:F.78, B:F.78, B:V.82, B:L.91, B:V.117, B:L.125, B:W.132, B:W.141, B:W.141, B:L.149, B:T.158, B:T.166, B:F.170 Hydrogen bonds: B:S.77, B:R.80, B:D.81, B:T.155, B:T.155, C:F.101 Water bridges: B:W.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luoma, A.M. et al., Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells. Immunity (2013)

Release Date

2013-12-18

Peptides

Beta-2-microglobulin: A
Cd1d1 protein: B
TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
E

Beta-2-microglobulin

Cd1d1 protein

TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region

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