SMTL ID : 6cug.1

Crystal structure of BC8B TCR-CD1b-PC complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.19, T.21, W.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.21 Water bridges: A:T.21

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.2: 26 residues within 4Å: Chain A: V.11, I.12, Q.13, S.28, H.37, W.39, A.46, F.48, V.62, Y.72, I.73, F.76, V.80, F.83, F.87, M.89, I.95, G.97, I.98, A.99, L.113, G.115, F.122, L.123, F.143 Ligands: POV.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.11, A:V.11, A:V.11, A:A.46, A:F.48, A:V.62, A:I.73, A:F.76, A:V.80, 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:F.122, A:F.122, A:F.122, A:F.143, A:F.143

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

POV.3: 32 residues within 4Å: Chain A: F.9, V.11, Y.72, G.75, F.76, E.79, A.99, G.100, L.113, L.123, V.125, C.130, F.143, I.147, G.152, I.153, M.154, T.156, V.157, L.160, L.161, T.164, C.165 Chain C: T.28, G.29, Y.30, P.31, P.94, S.95, G.96, Y.98 Ligands: CUY.2 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.9, A:V.11, A:Y.72, A:Y.72, A:F.76, A:E.79, A:A.99, A:L.113, A:L.113, A:L.123, A:V.125, A:F.143, A:I.147, A:I.147, A:I.153, A:T.156, A:L.160, A:L.161, A:T.164 Hydrogen bonds: A:G.152, A:T.156, C:Y.30, C:S.95 Water bridges: C:G.97

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

CL.4: 3 residues within 4Å: Chain D: A.2, G.3, D.26 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
T-cell receptor alpha variable TRAV9-2 - BC8B TCR: C
T-cell receptor beta variable TRBV6-2 - BC8B TCR: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

T-cell surface glycoprotein CD1b

Beta-2-microglobulin

T-cell receptor alpha variable TRAV9-2 - BC8B TCR

T-cell receptor beta variable TRBV6-2 - BC8B TCR

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