SMTL ID : 8dv3.1

Crystal structure of human CD1b presenting Phosphatidylinositol C34:1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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 Ligands: EDO.6, IOD.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.56, A:N.56, A:R.167 Hydrophobic interactions: A:L.170

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

NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: N.19, T.21, W.22 Ligands: EDO.13 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: P.92, F.93, E.94 Chain B: P.34 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.94 EDO.6: 2 residues within 4Å: Chain A: R.167 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain A: I.68, I.159 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.164, A:T.164 EDO.10: 3 residues within 4Å: Chain A: S.58, D.59, K.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.59, A:K.60 EDO.12: 4 residues within 4Å: Chain A: L.267, Q.270, D.271, I.272 No protein-ligand interaction detected (PLIP) EDO.13: 1 residues within 4Å: Ligands: NAG-NAG-FUC.2 No protein-ligand interaction detected (PLIP)

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

CL.4: 1 residues within 4Å: Chain A: R.70 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain A: G.55, N.56, F.57, R.167, Y.168, G.171, V.172 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: P.6, K.213 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: W.39, G.44 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: G.45, E.79, A.81 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: S.90 Ligand excluded by PLIP

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

NA.5: 4 residues within 4Å: Chain A: T.21, W.22, A.23, Q.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.23, A:Q.81 NA.18: 3 residues within 4Å: Chain A: S.195, P.196, G.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.195

1 x 6UL: TETRACOSYL PALMITATE(Non-covalent)

6UL.7: 23 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, V.80, F.83, F.87, M.89, I.95, G.97, I.98, L.113, F.122, L.123, F.143, L.146 Ligands: PIE.14 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.11, A:Q.13, A:H.37, A:A.46, A:F.69, A:F.69, A:F.69, A:F.69, A:Y.72, A:V.80, A:F.83, A:F.83, A:F.87, A:F.87, A:I.95, A:L.113, A:F.122, A:F.122, A:F.122, A:L.123, A:L.146

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

IOD.8: 2 residues within 4Å: Chain A: L.170 Ligands: NAG-NAG-BMA-MAN-MAN-FUC-FUC.1 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: R.139 Ligand excluded by PLIP

1 x PIE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL(Non-covalent)

PIE.14: 25 residues within 4Å: Chain A: F.48, L.65, I.68, V.71, Y.72, G.75, F.76, R.78, E.79, A.99, V.125, C.130, F.143, I.147, Q.151, G.152, I.153, M.154, T.156, V.157, L.160, L.161, C.165, Y.168 Ligands: 6UL.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.48, A:L.65, A:Y.72, A:F.76, A:E.79, A:A.99, A:V.125, A:F.143, A:I.147, A:I.153, A:T.156, A:V.157, A:L.160, A:L.161, A:Y.168, A:Y.168 Hydrogen bonds: A:Q.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Farquhar, R. et al., alpha beta T-cell receptor recognition of self-phosphatidylinositol presented by CD1b. J.Biol.Chem. (2023)

Release Date

2023-04-12

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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