SMTL ID : 3ubx.2 (1 other biounit)

Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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: 5 residues within 4Å: Chain A: W.23, S.24, R.25, N.42, R.79 No protein-ligand interaction detected (PLIP)

1 x 09N: (11Z,14Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide(Non-covalent)

09N.2: 27 residues within 4Å: Chain A: C.12, Q.14, S.28, V.30, W.40, I.47, F.70, Y.73, S.76, F.77, D.80, I.81, V.85, L.116, W.133, W.142, L.150, D.153, G.155, T.156, T.159, V.160, F.171 Chain C: Y.30, N.31, R.32, G.50 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Q.14, A:V.30, A:W.40, A:I.47, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:F.77, A:I.81, A:V.85, A:L.116, A:W.133, A:W.133, A:W.142, A:L.150, A:V.160, A:F.171 Hydrogen bonds: A:D.80, A:D.80, A:G.155, A:T.156, A:T.156, A:T.156, A:T.159, C:N.31, C:R.32

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

NAG.3: 3 residues within 4Å: Chain A: G.130, Q.161, N.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.161 Hydrogen bonds: A:Q.161, A:Q.161, A:N.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, E.D. et al., Structural basis for the recognition of C20:2-alpha GalCer by the invariant natural killer T cell receptor-like antibody L363. J.Biol.Chem. (2012)

Release Date

2011-11-16

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
L363 light chain (IGKV13-84*01): C
L363 heavy chain (IGHV9-4*02): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
I

D
G

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

L363 light chain (IGKV13-84*01)

L363 heavy chain (IGHV9-4*02)

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