SMTL ID : 3gmp.1

Structure of mouse CD1d in complex with PBS-25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 3 residues within 4Å: Chain A: W.23, S.24, 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: 9 residues within 4Å: Chain A: E.113, S.114, F.128, W.129, G.130, T.131, Q.161, L.164, N.165 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Q.134 Hydrophobic interactions: A:F.128, A:L.164 Hydrogen bonds: A:E.113, A:S.114, A:S.114, A:G.130

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

NAG.3: 4 residues within 4Å: Chain A: A.19, N.20, S.22, W.23 No protein-ligand interaction detected (PLIP)

1 x PBS: (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL(Non-covalent)

PBS.4: 19 residues within 4Å: Chain A: Y.73, S.76, R.79, D.80, L.84, I.98, L.100, L.116, V.118, F.120, W.133, W.142, L.143, L.150, D.153, G.155, T.156, T.159, V.160 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73, A:L.84, A:I.98, A:L.100, A:L.116, A:V.118, A:F.120, A:W.133, A:W.142, A:L.143, A:L.150, A:T.159, A:V.160 Hydrogen bonds: A:S.76, A:R.79, A:D.80, A:G.155, A:T.156, A:T.156 Water bridges: A:Y.73, A:D.153, A:G.155, A:T.156

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 9 residues within 4Å: Chain A: C.12, Q.14, S.28, W.40, F.70, Y.73, A.102, C.168, F.171 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.40, A:F.70, A:F.70, A:F.70, A:F.70, A:A.102, A:F.171 Hydrogen bonds: A:S.28

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: D.34, P.239, N.240, E.243, T.244, W.245 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.34, A:N.240, A:N.240, A:E.243, A:T.244 EDO.7: 6 residues within 4Å: Chain A: G.235, D.236, L.238, L.247, Q.248 Chain B: Q.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.8, B:Q.8 Hydrogen bonds: A:D.236, A:Q.248 EDO.8: 5 residues within 4Å: Chain A: W.31, P.239 Chain B: S.52, Y.63, L.65 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.52, B:S.52 Water bridges: B:Y.63, A:N.240 EDO.9: 7 residues within 4Å: Chain B: Q.8, V.9, V.93, Y.94, W.95, D.96, M.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.9, B:D.96, B:D.96 Water bridges: B:I.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiefner, A. et al., Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands. J.Mol.Biol. (2009)

Release Date

2009-11-10

Peptides

T-cell surface glycoprotein CD1d1: A
Beta-2 microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1d1

Beta-2 microglobulin

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