SMTL ID : 8glh.1

Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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.3 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- BMA- FUC- FUC: 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-FUC-FUC.2: 5 residues within 4Å: Chain A: T.18, N.19, S.20, T.21, W.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.18

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

IOD.3: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain B: G.45, E.79, A.81 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain B: S.90 Ligand excluded by PLIP

1 x 3IV: (11E)-hexadec-11-enoic acid(Non-covalent)

3IV.4: 16 residues within 4Å: Chain A: Q.13, Y.72, V.80, F.83, A.84, F.87, M.89, I.95, G.97, I.98, L.113, G.115, F.122, L.123, F.143 Ligands: 3IY.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.80, A:I.95, A:L.113, A:F.122, A:F.122, A:F.122, A:F.143, A:F.143, A:F.143

1 x 3IY: [(2~{R})-1-dodecanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] (8~{Z},11~{Z},14~{Z},24~{Z},27~{Z})-triaconta-8,11,14,24,27-pentaenoate(Non-covalent)

3IY.5: 29 residues within 4Å: Chain A: F.9, V.11, I.12, Q.13, G.27, S.28, H.37, A.46, L.65, E.67, I.68, F.69, V.71, Y.72, G.75, F.76, E.79, A.99, V.125, I.147, I.153, M.154, T.156, V.157, L.160, L.161, C.165, Y.168 Ligands: 3IV.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.9, A:V.11, A:Q.13, A:H.37, A:A.46, A:L.65, A:F.69, A:F.69, A:F.69, A:Y.72, A:F.76, A:E.79, A:A.99, A:V.125, A:I.147, A:I.153, A:T.156, A:L.160, A:L.160, A:L.161, A:Y.168

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

EDO.6: 4 residues within 4Å: Chain A: E.102, H.104, V.110, F.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.102 Water bridges: A:S.111 EDO.7: 5 residues within 4Å: Chain A: M.220, G.222, S.259, R.261, I.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.261, A:R.261 EDO.8: 2 residues within 4Å: Chain A: A.108, I.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.109 EDO.9: 6 residues within 4Å: Chain A: Q.88, M.89, K.90, P.92, F.93, R.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.88, A:K.90, A:P.92

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

NA.11: 5 residues within 4Å: Chain B: S.54, D.55, S.57, Y.65, L.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.54, B:D.55

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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