SMTL ID : 5wl1.1

Crystal Structure of Human CD1b in Complex with PG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 5 residues within 4Å: Chain A: T.18, N.19, T.21, W.22 Chain B: D.34 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:D.34, B:D.34, B:D.34 Hydrophobic interactions: A:W.22

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

NAG-NAG-BMA-MAN-FUC.2: 4 residues within 4Å: Chain A: N.127, A.128, S.129, R.158 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.128

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.3: 11 residues within 4Å: Chain A: N.56, F.57, S.58, E.61, I.109, P.166, R.167, L.170, G.171, N.174 Ligands: IOD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.174, A:L.170 Water bridges: A:R.167

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.4: 44 residues within 4Å: Chain A: F.9, V.11, I.12, Q.13, G.27, S.28, G.29, H.37, G.38, W.39, A.46, F.48, V.62, L.65, E.66, F.69, Y.72, I.73, F.76, E.79, V.80, F.83, A.84, F.87, M.89, F.93, I.95, Q.96, G.97, I.98, A.99, L.113, R.114, G.115, A.116, L.117, F.122, L.123, R.139, F.143, L.146, I.147, Y.150 Ligands: D3D.10 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Q.13, A:H.37, A:W.39, A:F.83, A:F.83, A:F.83, A:F.87, 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:L.146, A:I.147, A:Y.150

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

IOD.5: 4 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.3, NAG-NAG-BMA-MAN-MAN-FUC-FUC.3, NAG-NAG-BMA-MAN-MAN-FUC-FUC.3 Ligand excluded by PLIP

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

CL.6: 5 residues within 4Å: Chain A: W.39, S.41, G.44, R.70, I.73 Ligand excluded by PLIP

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

NA.7: 5 residues within 4Å: Chain A: G.257, L.258, Y.275, W.276, R.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.257, A:G.257, A:W.276 NA.12: 8 residues within 4Å: Chain A: W.30 Chain B: S.52, D.53, L.54, S.55, Y.63, L.64, L.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.52, B:D.53, B:S.55

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

EDO.8: 5 residues within 4Å: Chain A: K.50, D.179, R.182, N.239, W.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.50 EDO.9: 10 residues within 4Å: Chain A: S.191, S.192, G.193, P.194, V.204, H.206, R.245 Chain B: D.96, R.97, D.98 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.206, A:R.245, A:R.245, B:R.97 EDO.11: 8 residues within 4Å: Chain B: L.40, K.41, N.42, G.43, E.77, Y.78, A.79, K.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.40, B:G.43

1 x D3D: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate(Non-covalent)

D3D.10: 39 residues within 4Å: Chain A: F.9, V.11, H.37, F.48, S.53, K.54, F.57, V.62, L.65, E.67, I.68, F.69, V.71, Y.72, G.75, F.76, R.78, E.79, A.99, G.100, L.113, L.123, V.125, A.128, S.129, C.130, F.143, I.147, I.148, I.153, M.154, T.156, V.157, L.160, L.161, T.164, C.165, Y.168 Ligands: CUY.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.9, A:L.65, A:Y.72, A:I.147, A:V.157, A:V.157, A:L.160, A:Y.168, A:Y.168 Hydrogen bonds: A:T.156 Water bridges: A:I.68, A:T.156, A:T.156

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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