SMTL ID : 4ei5.1 (1 other biounit)

Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 10 residues within 4Å: Chain A: W.129, G.130, Q.161, M.162, N.165 Chain C: Y.33, F.52, S.53, D.54, K.68 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.54

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.2: 5 residues within 4Å: Chain A: S.22, S.24, N.42, D.43, R.74 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20

1 x FLC: CITRATE ANION(Non-covalent)

FLC.4: 7 residues within 4Å: Chain A: S.195, P.197, R.204, H.295, R.296, H.297 Chain B: D.98 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.195, A:R.204, A:R.204, A:H.297, B:D.98 Salt bridges: A:R.204, A:R.204, A:H.295, A:H.295, A:H.297, A:H.297

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.5: 24 residues within 4Å: Chain A: F.10, C.12, S.28, V.30, I.47, F.70, Y.73, S.76, F.77, D.80, L.100, V.118, W.133, L.150, G.155, T.156, T.159, V.160, L.163, C.168, F.171 Chain D: F.97, W.98, A.102 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.10, A:V.30, A:I.47, A:Y.73, A:Y.73, A:F.77, A:L.100, A:V.118, A:W.133, A:W.133, A:L.150, A:L.150, A:T.159, A:V.160, A:L.163, A:F.171, D:W.98 Hydrogen bonds: A:D.80, A:D.153, A:Q.154, A:G.155, A:T.156, A:T.156, A:T.156, D:W.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patel, O. et al., Recognition of CD1d-sulfatide mediated by a type II natural killer T cell antigen receptor. Nat.Immunol. (2012)

Release Date

2012-07-25

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain): C
Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)

Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)

Related Entries With Identical Sequence