SMTL ID : 7mxf.1

CD1c with antigen analogue 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: V.19, N.20, S.22, W.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.22, A:S.22 Water bridges: A:N.20, A:N.20

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

NHE.2: 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 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.238, A:P.238, B:Y.66 Hydrogen bonds: A:E.34 Water bridges: A:L.35, A:R.184, A:T.243 Salt bridges: A:R.184

1 x ZQ4: 2,6-anhydro-1-deoxy-1-[(S)-hydroxy{[(4R,8S,12R,16R,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-D-glycero-D-galacto-heptitol(Non-covalent)

ZQ4.3: 24 residues within 4Å: Chain A: F.10, V.12, I.13, Q.14, G.28, S.29, H.38, G.39, W.40, I.47, F.58, L.66, L.69, F.70, F.72, Y.73, G.154, V.155, T.158, L.162, I.163, T.166, C.167, F.170 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.10, A:V.12, A:Q.14, A:W.40, A:I.47, A:F.58, A:L.69, A:F.72, A:Y.73, A:Y.73, A:Y.73, A:V.155, A:V.155, A:T.158, A:L.162, A:L.162, A:I.163, A:T.166, A:F.170, A:F.170 Hydrogen bonds: A:G.154, A:T.158

1 x D12: DODECANE(Non-covalent)

D12.4: 7 residues within 4Å: Chain A: I.81, K.91, F.94, F.114, F.118, L.123, L.148 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.81, A:F.94, A:F.114, A:F.114, A:L.123, A:L.148

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

ZP7.5: 10 residues within 4Å: Chain A: F.72, L.77, E.80, I.81, H.84, S.143, V.144, L.148, Y.152, V.155 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.72, A:F.72, A:L.77, A:E.80, A:I.81, A:H.84, A:V.144, A:L.148, A:Y.152, A:Y.152, A:V.155 Hydrogen bonds: A:S.143 Water bridges: A:S.139, A:S.139

1 x MLA: MALONIC ACID(Non-covalent)

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

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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