SMTL ID : 3l9r.3 (3 other biounits)

Crystal structure of bovine CD1b3 with endogenously bound ligands

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-FUC-FUC.1: 6 residues within 4Å: Chain A: N.57, F.58, E.62, R.168, L.171, D.175 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.175, A:L.171

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

NAG.2: 1 residues within 4Å: Chain A: N.20 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: E.111, S.112, Q.127, N.128 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.111, A:Q.127 Water bridges: A:S.112

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: H.11, G.101, C.102, E.103, E.111, S.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.103, A:S.113

1 x L9R: (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

L9R.5: 20 residues within 4Å: Chain A: L.12, S.29, H.38, W.40, D.68, L.69, A.72, Y.73, F.74, G.76, F.77, E.80, V.81, I.96, V.98, A.100, F.123, F.144, I.154, L.161 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.12, A:L.12, A:H.38, A:W.40, A:L.69, A:Y.73, A:Y.73, A:Y.73, A:Y.73, A:F.74, A:F.74, A:F.77, A:F.77, A:E.80, A:V.81, A:I.96, A:I.96, A:V.98, A:F.123, A:F.144, A:F.144, A:L.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, E. et al., Crystal structure of bovine CD1b3 with endogenously bound ligands. J.Immunol. (2010)

Release Date

2010-06-16

Peptides

CD1b3: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

CD1b3

Beta-2-microglobulin

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