SMTL ID : 7mxh.1

CD1c with antigen analogue 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 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 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.20, A:N.20

1 x ZQ7: 2,6-anhydro-1-deoxy-1,1-difluoro-1-[(R)-hydroxy{[(4S,8S,12S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-D-glycero-D-galacto-heptitol(Non-covalent)

ZQ7.2: 19 residues within 4Å: Chain A: F.10, V.12, Q.14, G.30, H.38, W.40, I.47, L.66, L.69, F.70, F.72, Y.73, L.74, G.101, F.114, T.158, V.159, L.162, F.170 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.12, A:V.12, A:Q.14, A:W.40, A:I.47, A:L.66, A:L.69, A:F.70, A:F.70, A:Y.73, A:Y.73, A:Y.73, A:L.74, A:F.114, A:T.158, A:V.159, A:L.162, A:F.170

1 x D12: DODECANE(Non-covalent)

D12.3: 8 residues within 4Å: Chain A: Y.73, L.77, I.81, V.96, W.131, V.144, L.148 Ligands: ZP7.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.73, A:L.77, A:I.81, A:I.81, A:V.96, A:W.131, A:V.144, A:L.148

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

ZP7.4: 12 residues within 4Å: Chain A: F.72, Y.73, G.76, L.77, E.80, H.84, L.140, S.143, L.147, L.148, Y.152 Ligands: D12.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.72, A:L.77, A:L.147, A:L.148, A:Y.152 Hydrogen bonds: A:S.143 Salt bridges: A:H.84

2 x MLA: MALONIC ACID(Non-covalent)

MLA.5: 4 residues within 4Å: Chain A: H.183, R.184, Y.213, N.241 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.183 Hydrogen bonds: A:N.241 Salt bridges: A:R.184 MLA.6: 8 residues within 4Å: Chain B: T.76, E.77, K.78, D.79, W.98, D.99, R.100, D.101 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.100, B:D.101 Water bridges: B:D.79, B:Y.81 Salt bridges: B:R.100, B:R.100

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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