SMTL ID : 5wke.1

Crystal Structure of Human CD1b in Complex with PS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-FUC-NAG.1: 1 residues within 4Å: Chain A: N.127 No protein-ligand interaction detected (PLIP)

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.2: 6 residues within 4Å: Chain A: N.56, F.57, E.61, R.167, L.170, N.174 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.3: 27 residues within 4Å: Chain A: V.11, I.12, Q.13, S.28, H.37, W.39, A.46, E.66, F.69, Y.72, I.73, E.79, V.80, F.83, F.87, I.95, G.97, A.99, L.113, G.115, A.116, F.122, F.143, L.146, I.147, Y.150 Ligands: P50.12 26 PLIP interactions: 26 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:E.66, A:F.69, A:Y.72, A:I.73, A:E.79, A:V.80, A:F.83, A:F.83, A:F.83, A:F.87, A:F.87, A:I.95, A:A.99, A:L.113, A:F.122, A:F.122, A:F.122, A:F.143, A:I.147, A:Y.150

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

NAG.4: 3 residues within 4Å: Chain A: T.18, N.19, W.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.19, A:N.19

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

EDO.5: 7 residues within 4Å: Chain A: S.16, F.17, P.92, F.93, E.94 Chain B: P.32 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.17 EDO.6: 3 residues within 4Å: Chain A: S.58, D.59, K.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.58, A:D.59, A:K.60 EDO.16: 6 residues within 4Å: Chain A: I.98, R.114 Chain B: F.56, S.57, K.58, W.60 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.114, B:W.60

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

CL.7: 1 residues within 4Å: Chain A: F.87 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: W.189, L.190 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: V.110, S.111, Y.162 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: T.21, W.22, A.23, Q.81 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: F.93, E.94, G.118 Ligands: EDO.5 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: K.48, T.68, E.69 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: H.13, S.20 Ligands: NA.15 Ligand excluded by PLIP

1 x P50: (19S,22S,25R)-25-amino-22-hydroxy-16,22,26-trioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate(Non-covalent)

P50.12: 27 residues within 4Å: Chain A: F.9, H.37, F.57, V.62, L.65, E.67, I.68, F.69, V.71, Y.72, G.75, F.76, A.99, L.113, V.125, A.128, C.130, F.143, I.147, I.153, M.154, T.156, V.157, L.160, C.165, Y.168 Ligands: CUY.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.57, A:V.62, A:F.69, A:A.99, A:L.113, A:V.125, A:F.143, A:I.147, A:V.157, A:L.160, A:L.160, A:Y.168, A:Y.168, A:Y.168 Water bridges: A:I.68

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

NA.13: 5 residues within 4Å: Chain B: T.71, P.72, T.73, D.76, Y.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.73, B:T.73, B:Y.78 NA.14: 3 residues within 4Å: Chain A: H.206 Chain B: R.97, M.99 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.99 Water bridges: A:S.191 NA.15: 5 residues within 4Å: Chain B: S.20, N.21, F.22, E.69 Ligands: CL.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.21

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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