SMTL ID : 5fkp.1

Crystal structure of the mouse CD1d in complex with the p99 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: 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(Post Translational Modification)

NAG-NAG-BMA-MAN-FUC.1: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:S.114, A:S.114, A:G.130 Water bridges: A:W.129

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

NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.23, A:R.25 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:S.24, A:S.24 NAG.3: 3 residues within 4Å: Chain A: A.19, N.20, W.23 No protein-ligand interaction detected (PLIP)

1 x 6UL: TETRACOSYL PALMITATE(Non-covalent)

6UL.4: 12 residues within 4Å: Chain A: C.12, S.28, F.70, Y.73, L.100, A.102, W.133, L.150, L.163, T.167, C.168 Chain C: F.5 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.70, A:Y.73, A:A.102, A:W.133, A:L.150, A:T.167, C:F.5, C:F.5

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.31, D.34, P.239, N.240, E.243, T.244, W.245 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.240, A:N.240 Water bridges: A:D.34, A:E.243, A:E.243, A:E.243 GOL.6: 7 residues within 4Å: Chain A: W.31, N.240, A.241 Chain B: S.52, Y.63, L.65 Ligands: GOL.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.241, B:S.52 Water bridges: A:Q.36, B:S.52, B:S.52 GOL.7: 6 residues within 4Å: Chain A: P.217, V.218, W.219, K.266, H.267, S.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.268, A:S.268 GOL.8: 11 residues within 4Å: Chain A: W.192, H.209, Y.246, Q.248 Chain B: V.9, Y.10, S.11, P.15, W.95, D.96, M.99 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.209, A:Y.246, A:Y.246, B:S.11, B:D.96

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.9: 6 residues within 4Å: Chain B: I.35, E.36, I.37, M.51, M.54, I.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.37 Water bridges: B:H.34, B:I.35

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 Non-Classical Mhc Class I Molecule Cd1D. J.Biol.Chem. (2016)

Release Date

2016-03-30

Peptides

ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1: A
BETA 2 MICROGLOBULIN: B
P99: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1

BETA 2 MICROGLOBULIN

P99

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