SMTL ID : 7mx4.1

CD1c with antigen analogue 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-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.20, S.22, W.23 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.22, A:S.22 Water bridges: A:N.20, A:N.20, A:N.20

1 x ZPD: (4S,8R,12S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl (1R,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl hydrogen (R)-phosphate(Non-covalent)

ZPD.2: 22 residues within 4Å: Chain A: V.12, Q.14, G.28, S.29, H.38, G.39, I.47, F.58, L.66, F.70, F.72, Y.73, A.100, G.101, G.154, V.155, T.158, L.162, I.163, T.166, F.170 Ligands: ZP7.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.12, A:Q.14, A:H.38, A:I.47, A:F.58, A:L.66, A:F.70, A:F.70, A:F.72, A:Y.73, A:Y.73, A:Y.73, A:V.155, A:L.162, A:L.162, A:I.163, A:T.166, A:F.170, A:F.170 Hydrogen bonds: A:T.158

1 x D12: DODECANE(Non-covalent)

D12.3: 4 residues within 4Å: Chain A: I.81, F.118, V.144 Ligands: ZP7.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.81, A:F.118, A:V.144

1 x ZP7: (2S)-2,3-dihydroxypropyl hexadecanoate(Non-covalent)

ZP7.4: 11 residues within 4Å: Chain A: F.72, Y.73, L.77, E.80, H.84, S.139, S.143, L.148, Y.152 Ligands: ZPD.2, D12.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.72, A:Y.73, A:E.80, A:H.84, A:L.148, A:Y.152, A:Y.152

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.5: 9 residues within 4Å: Chain A: E.34, L.35, R.184, Y.213, P.238, G.242, W.244 Chain B: S.55, Y.66 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.238, A:P.238, A:W.244, B:Y.66 Hydrogen bonds: A:E.34 Water bridges: A:L.35, A:R.184, A:R.184, A:T.243 Salt bridges: A:R.184

2 x MLA: MALONIC ACID(Non-covalent)

MLA.6: 1 residues within 4Å: Chain A: P.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.135 MLA.7: 5 residues within 4Å: Chain A: A.240, N.241 Chain B: H.54, S.55, Y.70 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.70 Water bridges: B:D.56, B:D.56, A:N.239, A:G.242 Hydrogen bonds: A:Q.36, A:N.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reijneveld, J.F. et al., Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells. J.Biol.Chem. (2021)

Release Date

2021-11-17

Peptides

T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein

Beta-2-microglobulin

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