SMTL ID : 9oi0.1

Crystal structure of CD1b presenting ganglioside GD3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- FUC- 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-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC-FUC.1: 7 residues within 4Å: Chain A: N.54, F.55, E.59, R.165, L.168, N.172 Ligands: IOD.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.172, A:L.168 Water bridges: A:R.165

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: T.16, N.17, T.19, W.20 No protein-ligand interaction detected (PLIP)

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: L.168 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: A.176 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: R.137 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain B: G.45, E.79, A.81 Ligand excluded by PLIP

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

CL.6: 4 residues within 4Å: Chain A: Y.209, P.210, K.211, W.240 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: W.37, G.42 Ligand excluded by PLIP

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

EDO.7: 7 residues within 4Å: Chain A: W.274, R.275, G.276, S.277, G.278, L.279, N.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.276, A:G.278, A:L.279 Water bridges: A:S.277, A:S.277 EDO.8: 3 residues within 4Å: Chain A: F.110, R.112, K.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.112, A:R.112 Water bridges: A:L.111 EDO.10: 5 residues within 4Å: Chain A: I.96, R.112 Chain B: S.59, K.60, W.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.59, B:K.60

1 x 01: N-{(2S,3R,4E)-1-[(4-O-beta-D-galactopyranosyl-beta-D-glucopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}octadecanamide

01.11: 24 residues within 4Å: Chain A: F.7, L.63, V.69, Y.70, G.73, F.74, E.77, A.97, L.111, L.121, V.123, C.128, F.141, I.145, Q.149, G.150, I.151, M.152, T.154, V.155, L.158, C.163, Y.166 Ligands: CUY.12 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.63, A:Y.70, A:Y.70, A:Y.70, A:F.74, A:F.74, A:E.77, A:A.97, A:L.111, A:L.121, A:V.123, A:F.141, A:F.141, A:I.145, A:T.154, A:V.155, A:L.158, A:L.158, A:Y.166, A:Y.166 Hydrogen bonds: A:Q.149

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.12: 27 residues within 4Å: Chain A: V.9, Q.11, S.26, H.35, W.37, A.44, F.67, Y.70, I.71, V.78, F.81, F.85, M.87, I.93, Q.94, G.95, I.96, A.97, L.111, R.112, G.113, A.114, F.120, L.121, F.141, L.144 Ligands: 01.11 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.9, A:V.9, A:Q.11, A:H.35, A:W.37, A:F.67, A:Y.70, A:I.71, A:V.78, A:V.78, A:F.81, A:F.85, A:F.85, A:F.85, A:I.93, A:I.93, A:A.97, A:F.120, A:F.120, A:F.120, A:L.121, A:L.144 Hydrogen bonds: A:Y.70

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 1 residues within 4Å: Chain A: R.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, T.P., Crystal structure of CD1b presenting ganglioside GD3. To Be Published

Release Date

2025-11-19

Peptides

T-cell surface glycoprotein CD1b: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1b

Beta-2-microglobulin