SMTL ID : 5efi.1

Crystal structure of mouse CD1d in complex with the p99p lipopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-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: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-FUC.2: 7 residues within 4Å: Chain A: E.113, S.114, W.129, G.130, T.131, Q.161, N.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.114, A:S.114, A:G.130

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 CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 9 residues within 4Å: Chain A: C.12, Q.14, S.28, W.40, F.70, Y.73, R.74 Ligands: NA.5, PLM.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.70, A:Y.73 Hydrogen bonds: A:S.28, A:S.28

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: T.26, D.27, S.28, W.40, S.41, R.74 Ligands: CIT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.28, A:S.28, A:R.74

1 x PLM: PALMITIC ACID(Covalent)

PLM.6: 8 residues within 4Å: Chain A: Y.73, A.102, T.159, L.163, C.168, F.171 Chain C: K.11 Ligands: CIT.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73, A:A.102, A:F.171

1 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.7: 5 residues within 4Å: Chain A: Y.73, V.118, W.133 Chain C: F.5, I.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.118, A:W.133, C:F.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girardi, E. et al., Structure of an alpha-Helical Peptide and Lipopeptide Bound to the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule CD1d. J.Biol.Chem. (2016)

Release Date

2016-03-30

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
p99p: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

p99p

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