SMTL ID : 9ohv.1

CD1c presenting dual lipids MPM and GD3 ganglioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: V.15, N.16, W.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16

1 x 01: (2R,3R,4E)-3-hydroxy-2-octadecanamidooctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-L-glycero-beta-L-altro-non-2-ulopyranonosyl-(2->8)-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside

01.2: 26 residues within 4Å: Chain A: Q.17, Y.69, G.72, L.73, E.76, I.77, H.80, A.81, S.82, Q.83, D.84, Y.85, S.86, K.87, F.90, F.110, V.112, F.114, L.119, W.127, L.136, S.139, V.140, L.143, L.144, Y.148 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Y.69, A:E.76, A:I.77, A:I.77, A:I.77, A:H.80, A:A.81, A:K.87, A:F.90, A:F.90, A:F.110, A:F.110, A:V.112, A:V.112, A:F.114, A:L.119, A:W.127, A:V.140, A:L.143, A:L.144, A:Y.148 Hydrogen bonds: A:Q.17, A:S.82, A:S.82, A:Q.83, A:D.84, A:Y.85, A:S.86, A:K.87, A:S.139

1 x MK0: 1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose(Non-covalent)

MK0.3: 28 residues within 4Å: Chain A: F.6, V.8, Q.10, G.24, S.25, H.34, W.36, I.43, L.62, L.65, F.66, F.68, Y.69, L.70, A.96, G.97, F.110, E.149, G.150, V.151, E.153, T.154, V.155, L.158, I.159, T.162, C.163, F.166 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.6, A:V.8, A:Q.10, A:H.34, A:W.36, A:W.36, A:I.43, A:I.43, A:L.62, A:L.65, A:F.66, A:F.66, A:F.66, A:Y.69, A:Y.69, A:Y.69, A:L.70, A:T.154, A:V.155, A:I.159, A:T.162, A:F.166, A:F.166 Hydrogen bonds: A:E.153

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

CL.4: 1 residues within 4Å: Chain A: Y.209 Ligand excluded by PLIP

1 x KZF: 2-(cyclohexylazaniumyl)ethanesulfonate(Non-covalent)

KZF.5: 9 residues within 4Å: Chain A: L.28, D.29, L.31, L.171, V.178, Y.209, P.210, K.211, P.212 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.28, A:D.29, A:L.31, A:L.31, A:L.171, A:V.178, A:V.178 Hydrogen bonds: A:D.29, A:Y.209, A:K.211 Water bridges: A:E.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, T.P. et al., CD1c presenting dual lipids MPM and GD3 ganglioside. To Be Published

Release Date

2025-11-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein

Beta-2-microglobulin

Related Entries With Identical Sequence