SMTL ID : 8glf.1

Crystal Structure of Human CD1b in Complex with Sphingomyelin C34:2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

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

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.2: 7 residues within 4Å: Chain A: N.56, F.57, E.61, R.167, L.170, N.174 Ligands: IOD.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.170, A:N.174

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

EDO.3: 3 residues within 4Å: Chain A: G.5, T.7, D.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.5, A:T.7 EDO.4: 5 residues within 4Å: Chain A: F.83, F.87, R.139, K.142, F.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.87

1 x 3LY: [(~{Z},2~{R},3~{S})-2-(hexadecanoylamino)-3-oxidanyl-octadec-4-enyl] 2-(trimethyl-$l^{4}-azanyl)ethyl hydrogen phosphate(Non-covalent)

3LY.5: 18 residues within 4Å: Chain A: F.9, L.65, I.68, Y.72, G.75, F.76, A.99, I.147, Y.150, Q.151, G.152, I.153, T.156, V.157, L.160, L.161, C.165 Ligands: 6UL.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.9, A:L.65, A:I.68, A:Y.72, A:Y.72, A:A.99, A:Y.150, A:T.156, A:V.157, A:L.161 Hydrogen bonds: A:Q.151, A:T.156

1 x 6UL: TETRACOSYL PALMITATE(Non-covalent)

6UL.6: 18 residues within 4Å: Chain A: V.11, I.12, Q.13, H.37, W.39, A.46, F.69, Y.72, F.76, I.95, G.97, I.98, L.113, R.114, G.115, F.122, F.143 Ligands: 3LY.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.11, A:H.37, A:A.46, A:F.69, A:F.69, A:I.95, A:I.95, A:F.122, A:F.122, A:F.143

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

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: W.39, G.44 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: A.188 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: Y.211, K.213 Ligand excluded by PLIP

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

IOD.11: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.2 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain B: G.45, E.79, A.81 Ligand excluded by PLIP

1 x NI: NICKEL (II) ION(Non-covalent)

NI.13: 1 residues within 4Å: Chain B: S.90 No protein-ligand interaction detected (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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