SMTL ID : 5wkg.1

Crystal Structure of Human CD1b in Complex with PA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 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.12 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: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 1 residues within 4Å: Chain A: N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.127

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

NAG.3: 3 residues within 4Å: Chain A: T.18, N.19, W.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.18

1 x D21: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate(Non-covalent)

D21.4: 23 residues within 4Å: Chain A: F.9, V.62, L.65, I.68, V.71, Y.72, G.75, F.76, A.99, V.125, A.128, S.129, C.130, F.143, I.147, I.153, M.154, T.156, V.157, L.160, L.161, Y.168 Ligands: CUY.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.9, A:V.62, A:L.65, A:Y.72, A:Y.72, A:F.76, A:A.99, A:V.125, A:F.143, A:I.147, A:I.153, A:V.157, A:V.157, A:L.160, A:L.161, A:Y.168, A:Y.168, A:Y.168 Hydrogen bonds: A:T.156

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.5: 28 residues within 4Å: Chain A: V.11, I.12, Q.13, G.27, S.28, H.37, W.39, A.46, F.69, Y.72, I.73, F.76, E.79, V.80, F.83, F.87, I.95, G.97, I.98, L.113, G.115, F.122, L.123, F.143, L.146, Y.150, I.153 Ligands: D21.4 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:Q.13, A:W.39, A:A.46, A:F.69, A:F.69, A:F.69, A:I.73, A:F.76, A:E.79, A:F.83, A:F.83, 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:F.143, A:L.146, A:Y.150, A:Y.150, A:I.153

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 10 residues within 4Å: Chain A: G.5, P.6, D.32, D.33, L.34, Y.211, P.212, K.213, P.214, W.242 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.5, A:D.33, A:D.33, A:Y.211, A:K.213 Water bridges: A:G.5, A:D.32, A:D.32

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

CL.7: 3 residues within 4Å: Chain A: V.110, S.111, Y.162 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: Q.4 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: W.276, G.280, N.282 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: K.6, I.7 Ligand excluded by PLIP

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

EDO.10: 6 residues within 4Å: Chain A: S.16, F.17, P.92, F.93, E.94 Chain B: P.32 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.17, A:F.17, A:F.93, A:E.94 Water bridges: A:E.94

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

IOD.11: 2 residues within 4Å: Chain A: F.87, K.142 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain B: N.42, G.43, E.77, A.79 Ligand excluded by PLIP

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

NA.13: 3 residues within 4Å: Chain B: N.83, H.84, L.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.83, B:N.83, B:H.84, B:L.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shahine, A. et al., A molecular basis of human T cell receptor autoreactivity toward self-phospholipids. Sci Immunol (2017)

Release Date

2017-11-01

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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