SMTL ID : 7sh4.1

CD1a-phosphatidylglycerol binary structure

Coordinates

PDB Format

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: 2 residues within 4Å: Chain A: N.57, E.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.57 Water bridges: A:N.57, A:N.57

1 x MW9: (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate(Non-covalent)

MW9.2: 34 residues within 4Å: Chain A: F.10, V.12, W.14, A.16, N.26, V.28, S.29, G.30, H.38, T.39, W.40, I.47, W.63, F.70, R.73, T.74, R.76, S.77, F.78, G.80, I.81, I.96, V.98, G.100, L.114, L.116, W.131, V.147, L.148, Q.150, E.154, L.162, C.166, F.169 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.10, A:V.12, A:W.14, A:W.14, A:W.14, A:A.16, A:V.28, A:H.38, A:I.47, A:W.63, A:R.73, A:T.74, A:F.78, A:I.81, A:I.81, A:V.98, A:L.114, A:L.116, A:V.147, A:L.162, A:F.169 Hydrogen bonds: A:Q.150, A:E.154, A:E.154 Salt bridges: A:R.73, A:R.73, A:R.76

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

EDO.3: 6 residues within 4Å: Chain A: G.233, D.234, L.236, L.245, R.246 Chain B: Q.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.234, A:D.234, A:R.246 Water bridges: B:Q.9 EDO.5: 8 residues within 4Å: Chain A: S.238, A.239, D.240 Chain B: R.13, F.23, N.25, L.66, Y.68 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.239, A:D.240, B:R.13, B:N.25 Water bridges: A:D.240

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

MES.4: 6 residues within 4Å: Chain A: Q.115, D.122, Y.134 Chain B: K.59, D.60, W.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.134 Water bridges: A:D.122, A:D.122 Salt bridges: A:D.122

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

PEG.6: 5 residues within 4Å: Chain B: V.38, D.39, V.50, H.52, Y.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.39 Water bridges: B:L.40 PEG.7: 9 residues within 4Å: Chain A: H.11, I.13, W.31, T.99 Chain B: S.56, F.57, S.58, K.59, Y.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.64, B:Y.64 Water bridges: B:S.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monnot, G.C. et al., Staphylococcal phosphatidylglycerol antigens activate human T cells via CD1a. Nat.Immunol. (2023)

Release Date

2022-10-05

Peptides

T-cell surface glycoprotein CD1a: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1a

Beta-2-microglobulin

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