SMTL ID : 6c09.1

Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 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: 2 residues within 4Å: Chain A: N.23, W.26 No protein-ligand interaction detected (PLIP)

1 x EKG: (2R)-2,3-dihydroxypropyl hexadecanoate(Non-covalent)

EKG.2: 20 residues within 4Å: Chain A: F.13, V.15, I.16, Q.17, F.19, G.29, Q.30, G.31, S.32, G.33, H.41, W.43, S.45, I.50, L.69, F.73, L.77, L.165, C.170, F.173 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.13, A:Q.17, A:H.41, A:W.43, A:I.50, A:L.69, A:F.73, A:L.165, A:F.173, A:F.173

2 x D10: DECANE(Non-covalent)

D10.3: 5 residues within 4Å: Chain A: L.80, I.84, V.119, L.126, L.127 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.80, A:I.84, A:V.119, A:L.126, A:L.127 D10.4: 8 residues within 4Å: Chain A: G.79, L.80, E.83, H.87, L.150, L.151, Y.155 Chain D: Y.98 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:Y.98, A:E.83, A:L.150, A:L.151, A:Y.155, A:Y.155

3 x K: POTASSIUM ION(Non-covalent)

K.5: 2 residues within 4Å: Chain A: D.244 Chain B: R.15 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.244 K.6: 4 residues within 4Å: Chain A: K.235, G.237, Q.250, I.252 No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain D: S.97, R.99, R.102, E.105 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:R.102

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

EDO.7: 6 residues within 4Å: Chain C: P.45, T.46, F.47 Chain D: Q.106, F.107, F.108 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.106, D:F.108, C:F.47 EDO.8: 3 residues within 4Å: Chain C: K.57, N.58, E.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.59 EDO.9: 8 residues within 4Å: Chain C: N.8, S.9, L.12, I.21, L.22, N.23, T.105 Ligands: PEG.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.7, C:I.21, C:N.23, C:N.23

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 5 residues within 4Å: Chain C: Q.7, N.8, N.23, D.25 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.8, C:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wun, K.S. et al., T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids. Nat. Immunol. (2018)

Release Date

2018-03-21

Peptides

T-cell surface glycoprotein CD1c: A
Beta-2-microglobulin: B
3C8 T cell receptor alpha-chain: C
3C8 T cell receptor beta-chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

T-cell surface glycoprotein CD1c

Beta-2-microglobulin

3C8 T cell receptor alpha-chain

3C8 T cell receptor beta-chain

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