SMTL ID : 8gle.1

Crystal Structure of Human CD1b in Complex with Lysosulfatide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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.56, F.57, E.61, R.167, L.170, N.174 Ligands: IOD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.174, A:L.170 Water bridges: A:R.167

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.18, N.19, T.21, W.22 No protein-ligand interaction detected (PLIP)

1 x SGF: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside(Non-covalent)

SGF.3: 15 residues within 4Å: Chain A: F.9, H.37, V.62, L.65, V.71, Y.72, A.99, L.113, I.153, T.156, V.157, L.160, C.165, Y.168 Ligands: CUY.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.62, A:L.65, A:A.99, A:L.113, A:L.160, A:Y.168 Hydrogen bonds: A:T.156

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.4: 27 residues within 4Å: Chain A: V.11, I.12, Q.13, G.27, H.37, F.69, Y.72, E.79, V.80, F.83, F.87, M.89, I.95, Q.96, G.97, I.98, L.113, G.115, A.116, F.122, L.123, F.143, L.146, I.147, Y.150 Ligands: SGF.3, EDO.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:Q.13, A:H.37, A:F.69, A:F.69, A:F.69, A:F.83, A:F.83, A:F.87, A:F.87, A:I.95, A:I.95, A:L.113, A:F.122, A:F.122, A:F.122, A:F.143, A:L.146, A:I.147, A:Y.150

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

IOD.5: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP

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

EDO.6: 2 residues within 4Å: Chain A: V.125 Ligands: CUY.4 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: P.92, F.93, E.94 Chain B: P.34 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.35, A:E.94 Hydrogen bonds: A:P.92 EDO.8: 6 residues within 4Å: Chain A: G.5, P.6, Y.211, P.212, K.213, P.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.213 Water bridges: A:G.5 EDO.11: 3 residues within 4Å: Chain B: L.89, S.90, Q.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.90, B:Q.91

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

CL.9: 1 residues within 4Å: Chain A: R.70 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: W.39, G.44 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: N.44, G.45, E.79, A.81 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, S. et al., CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms. Cell (2023)

Release Date

2023-09-20

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

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