SMTL ID : 6c15.1

CD1c in complex with phosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: V.22, N.23, W.26 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: N.60, R.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.60 NAG.3: 2 residues within 4Å: Chain A: N.131, T.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.131

1 x D12: DODECANE(Non-covalent)

D12.4: 11 residues within 4Å: Chain A: Y.76, L.80, I.84, F.117, V.119, F.121, L.143, V.147, L.151, V.158 Ligands: 6PL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.76, A:L.80, A:I.84, A:F.117, A:V.119, A:V.119, A:F.121, A:L.143, A:L.151, A:L.151, A:V.158

1 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.5: 25 residues within 4Å: Chain A: F.13, V.15, I.50, L.69, L.72, F.73, F.75, Y.76, L.80, H.87, F.117, L.143, S.146, V.147, L.150, L.151, Y.155, V.158, T.161, V.162, L.165, T.169, C.170, F.173 Ligands: D12.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.13, A:V.15, A:I.50, A:L.69, A:F.73, A:F.73, A:F.73, A:Y.76, A:Y.76, A:L.80, A:F.117, A:L.143, A:V.147, A:L.151, A:Y.155, A:V.158, A:T.169, A:F.173 Hydrogen bonds: A:T.161

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

NA.6: 3 residues within 4Å: Chain A: E.156, T.159, E.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.156, A:E.160

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: K.235, G.237, D.238, Q.250 Chain B: Q.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.238 Salt bridges: A:K.235

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.8: 4 residues within 4Å: Chain A: C.140, G.141, S.142, L.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.142

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

EDO.9: 3 residues within 4Å: Chain A: L.201, G.202, S.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.201, A:S.203

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 4 residues within 4Å: Chain A: L.207, K.235, I.252, E.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.254

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1c

Beta-2-microglobulin

Related Entries With Identical Sequence