SMTL ID : 8glg.1

Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.174, A:L.170 Water bridges: A:R.167

1 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.2: 3 residues within 4Å: Chain A: T.18, N.19, W.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.22

1 x L9Q: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

L9Q.3: 23 residues within 4Å: Chain A: F.9, H.37, L.65, E.67, I.68, V.71, Y.72, G.75, F.76, A.99, L.113, V.125, C.130, F.143, I.147, I.153, M.154, T.156, V.157, L.160, L.161, Y.168 Ligands: CUY.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.65, A:I.68, A:L.113, A:V.125, A:I.147, A:I.153, A:V.157, A:L.160, A:L.161, A:Y.168, A:Y.168 Hydrogen bonds: A:E.67 Water bridges: A:E.67, A:I.68, A:T.156, A:T.156

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

NI.4: 3 residues within 4Å: Chain A: F.87, Q.88, K.142 No protein-ligand interaction detected (PLIP)

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.5: 30 residues within 4Å: Chain A: V.11, I.12, Q.13, G.27, S.28, H.37, W.39, A.46, E.66, F.69, Y.72, E.79, V.80, F.83, F.87, M.89, I.95, G.97, I.98, A.99, L.113, G.115, A.116, F.122, L.123, F.143, L.146, I.147, Y.150 Ligands: L9Q.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:H.37, A:W.39, A:E.66, A:F.69, A:F.69, A:Y.72, A:E.79, A:F.83, A:F.83, A:F.83, A:F.87, A:F.87, A:I.95, A:I.95, A:A.99, A:L.113, A:F.122, A:F.122, A:F.122, A:F.143, A:F.143, A:I.147, A:Y.150

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

CL.6: 2 residues within 4Å: Chain A: W.39, G.44 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: W.189, L.190 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: Y.211, K.213 Ligand excluded by PLIP

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

IOD.10: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain B: G.45, E.79, A.81 Ligand excluded by PLIP

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

EDO.11: 3 residues within 4Å: Chain A: I.68, T.156, I.159 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: P.92, F.93, E.94 Chain B: P.34 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:D.36, A:E.94, A:E.94, A:E.94, A:E.94 Hydrogen bonds: A:P.92 EDO.14: 3 residues within 4Å: Chain B: S.54, L.67, Y.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.69 Water bridges: B:S.54, B:S.54 EDO.15: 4 residues within 4Å: Chain B: T.88, L.89, S.90, Q.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.88, B:S.90, B:Q.91 Water bridges: B:Q.91

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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