SMTL ID : 3l9r.4 (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: 8 residues within 4Å: Chain A: N.57, F.58, E.62, P.167, R.168, L.171, G.172, D.175 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.175, A:P.167, A:L.171 Water bridges: A:R.168

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

NAG.2: 3 residues within 4Å: Chain A: S.112, Q.127, N.128 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.127 Water bridges: A:S.112

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: H.11, G.101, C.102, E.103, E.111, S.112, S.113, R.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.111, A:S.113 GOL.4: 3 residues within 4Å: Chain A: E.188, A.189, I.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.189, A:A.189 GOL.5: 2 residues within 4Å: Chain A: E.91, R.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.91, A:R.140, A:R.140 GOL.6: 6 residues within 4Å: Chain A: P.215, V.216, R.217, K.264, H.265, S.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.266

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: Y.151, Q.152, G.153, I.154 Ligand excluded by PLIP

1 x L9Q: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

L9Q.8: 25 residues within 4Å: Chain A: L.12, M.13, Q.14, S.29, H.38, W.40, L.69, A.72, Y.73, F.74, I.75, G.76, F.77, R.79, E.80, F.88, L.90, I.96, V.98, F.123, F.144, I.154, I.157, I.158, L.161 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.12, A:L.12, A:H.38, A:W.40, A:Y.73, A:Y.73, A:F.74, A:F.74, A:E.80, A:F.88, A:L.90, A:I.96, A:I.96, A:V.98, A:F.123, A:F.123, A:I.154, A:I.157, A:I.158, A:I.158, A:L.161 Hydrogen bonds: A:R.79, A:E.80 Water bridges: A:R.71, A:A.72

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
G

B
H

CD1b3

Beta-2-microglobulin

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