SMTL ID : 8gli.1

Crystal Structure of Human CD1b in Complex with Mycobacterial C85-GMM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: 6 residues within 4Å: Chain A: N.56, F.57, E.61, R.167, L.170 Ligands: IOD.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.56, A:R.167 Hydrophobic interactions: A:L.170

1 x ZR2: 6-O-[(2R,3R)-3-hydroxy-20-{(1R,2S)-2-[(17R,18R)-17-methoxy-18-methyldotriacontyl]cyclopropyl}-2-pentadecylicosanoyl]-alpha-L-galactopyranose(Non-covalent)

ZR2.2: 44 residues within 4Å: Chain A: F.9, V.11, I.12, Q.13, G.27, S.28, H.37, W.39, A.46, F.48, L.65, I.68, F.69, V.71, Y.72, I.73, G.75, F.76, E.79, V.80, F.83, F.87, M.89, I.95, Q.96, G.97, I.98, A.99, L.113, G.115, A.116, F.122, L.123, V.125, F.143, L.146, I.147, I.153, T.156, V.157, L.160, L.161, C.165, Y.168 41 PLIP interactions: 41 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:Q.13, A:H.37, A:W.39, A:A.46, A:A.46, A:F.48, A:L.65, A:F.69, A:V.71, A:Y.72, A:Y.72, A:Y.72, A:I.73, A:I.73, A:F.76, A:F.76, A:E.79, A:F.83, A:F.87, 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:L.123, A:V.125, A:L.146, A:I.153, A:I.153, A:T.156, A:V.157, A:L.160, A:L.160, A:Y.168 Hydrogen bonds: A:I.68, A:T.156

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.127, Y.162 No protein-ligand interaction detected (PLIP)

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

CL.4: 1 residues within 4Å: Chain A: L.190 Ligand excluded by PLIP

3 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 IOD.6: 4 residues within 4Å: Chain B: N.44, G.45, E.79, A.81 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain B: T.73 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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