SMTL ID : 2gaz.1

Mycobacterial lipoglycan presentation by CD1d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: A.19, N.20, W.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:N.20 NAG.3: 3 residues within 4Å: Chain A: W.23, S.24, N.42 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.23 Hydrogen bonds: A:S.24, A:N.42 Water bridges: A:D.43

1 x XPX: (2R)-3-[(HYDROXY{[(2R,3R,5S,6R)-3,4,5-TRIHYDROXY-2,6-BIS(ALPHA-D-MANNOPYRANOSYLOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]PROPAN E-1,2-DIYL DIHEXADECANOATE(Non-covalent)

XPX.4: 26 residues within 4Å: Chain A: F.10, C.12, M.69, F.70, V.72, Y.73, S.76, F.77, R.79, D.80, L.84, I.98, A.102, V.118, F.120, W.133, W.142, L.143, D.153, G.155, T.156, T.159, V.160, L.163, L.164, F.171 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.10, A:F.70, A:Y.73, A:F.77, A:I.98, A:A.102, A:V.118, A:F.120, A:F.120, A:W.133, A:W.133, A:W.142, A:L.143, A:V.160, A:L.163, A:L.164, A:F.171, A:F.171 Hydrogen bonds: A:S.76, A:S.76, A:D.153, A:D.153, A:T.156, A:T.156, A:T.159 Salt bridges: A:R.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zajonc, D.M. et al., Structural characterization of mycobacterial phosphatidylinositol mannoside binding to mouse CD1d. J.Immunol. (2006)

Release Date

2006-09-26

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

Related Entries With Identical Sequence