SMTL ID : 6d64.1

Crystal Structure of Human CD1b in Complex with POPC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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.15 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- 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.2: 3 residues within 4Å: Chain A: T.18, N.19, W.22 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.3: 1 residues within 4Å: Chain A: N.127 No protein-ligand interaction detected (PLIP)

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.4: 24 residues within 4Å: Chain A: F.9, L.65, I.68, V.71, Y.72, G.75, F.76, R.78, A.99, V.125, A.128, C.130, F.143, I.147, Q.151, G.152, 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: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.147, A:I.153, A:T.156, A:V.157, A:V.157, A:L.161, A:Y.168, A:Y.168, A:Y.168 Hydrogen bonds: A:R.78

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.5: 25 residues within 4Å: Chain A: V.11, I.12, Q.13, S.28, W.39, F.69, Y.72, V.80, F.83, F.87, M.89, I.95, G.97, I.98, A.99, L.113, G.115, A.116, F.122, L.123, F.143, L.146, I.147, Y.150 Ligands: POV.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:V.11, A:Q.13, A:W.39, A:F.69, A:F.69, A:F.69, A:F.83, A:F.83, 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:F.143, A:I.147, A:Y.150

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

CL.6: 2 residues within 4Å: Chain A: W.39, G.44 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: W.189, L.190 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.114, D.121 Chain B: K.60 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: Q.227 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: F.87, K.142 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: G.45, E.79, A.81 Ligand excluded by PLIP

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

EDO.12: 4 residues within 4Å: Chain A: P.92, F.93, E.94 Chain B: P.34 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.92 Water bridges: A:E.94, A:E.94, A:E.94, A:E.94 EDO.13: 2 residues within 4Å: Chain A: T.21 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.20 EDO.18: 4 residues within 4Å: Chain B: T.88, L.89, S.90, Q.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.88, B:S.90, B:Q.91

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

NA.14: 2 residues within 4Å: Chain A: S.20 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.20, A:Q.81, A:D.82, A:G.85

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

IOD.15: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: Y.211, K.213 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shahine, A. et al., A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids. Nat Commun (2019)

Release Date

2019-01-16

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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