SMTL ID : 4ono.1

CD1c in complex with PM (phosphomycoketide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

monomer

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: 3 residues within 4Å: Chain A: V.134, N.135, W.138 No protein-ligand interaction detected (PLIP)

1 x PMK: (4R,8S,16S,20R)-4,8,12,16,20-pentamethylheptacosyl dihydrogen phosphate(Non-covalent)

PMK.2: 34 residues within 4Å: Chain A: F.125, V.127, I.128, Q.129, F.131, G.141, Q.142, G.143, S.144, G.145, H.153, G.154, W.155, S.157, I.162, F.164, L.178, L.181, L.184, F.185, Y.188, L.189, G.191, L.192, A.215, G.216, F.229, V.270, T.273, V.274, L.277, T.281, C.282, F.285 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.125, A:V.127, A:Q.129, A:H.153, A:W.155, A:W.155, A:I.162, A:I.162, A:I.162, A:F.185, A:F.185, A:F.185, A:Y.188, A:Y.188, A:L.189, A:L.189, A:A.215, A:F.229, A:V.274, A:F.285 Hydrogen bonds: A:L.192

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

CL.3: 3 residues within 4Å: Chain A: S.280, T.281, R.284 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Q.9, G.349, D.350, R.362 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: K.49 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: S.308 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: Y.328, P.329, K.330, W.359 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: W.96, D.97, R.98 Ligand excluded by PLIP

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.9: 8 residues within 4Å: Chain A: S.312, P.313, G.314, P.315, G.316, R.317, L.318, D.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.312, A:G.314, A:G.316, A:R.317 MLI.10: 7 residues within 4Å: Chain A: P.15, A.16, R.98, D.99, W.306, L.307, S.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.16, A:R.98, A:L.307 MLI.11: 3 residues within 4Å: Chain A: T.5, P.6, K.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, S. et al., Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by alpha beta T cells. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-10-08

Peptides

Beta-2-microglobulin/T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-2-microglobulin/T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein