SMTL ID : 6xng.1

MHC-like protein complex structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: A.19, N.20, W.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.23 NAG-NAG.2: 4 residues within 4Å: Chain A: W.23, S.24, R.25, N.42 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: W.129, G.130, T.131, Q.161, N.165 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.134

2 x V8P: (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxyheptadecan-2-yl]-3-hydroxyheptadecanamide(Non-covalent)

V8P.4: 10 residues within 4Å: Chain A: F.10, V.30, W.63, L.66, F.70, A.102, L.163, C.168, F.171 Ligands: V8P.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.10, A:F.10, A:V.30, A:W.63, A:L.66, A:F.70, A:A.102, A:L.163, A:F.171, A:F.171 V8P.5: 30 residues within 4Å: Chain A: Q.14, S.28, W.40, M.69, F.70, Y.73, S.76, F.77, D.80, L.84, M.88, L.100, A.102, V.118, F.120, W.133, L.143, L.150, D.153, G.155, T.156, T.159, V.160, L.163 Chain C: P.28, N.30, D.93, R.94, G.95 Ligands: V8P.4 31 PLIP interactions: 26 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Q.14, A:Q.14, A:F.70, A:Y.73, A:F.77, A:F.77, A:L.84, A:L.100, A:L.100, A:A.102, A:V.118, A:F.120, A:W.133, A:L.143, A:L.150, A:L.150, A:T.156, A:V.160, A:L.163 Hydrogen bonds: A:D.80, A:D.153, A:G.155, A:T.156, A:T.156, A:T.156, A:T.159, C:N.30, C:G.95 Water bridges: C:N.30, C:K.67 Salt bridges: C:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, S.F. et al., Host immunomodulatory lipids created by symbionts from dietary amino acids. Nature (2021)

Release Date

2021-11-10

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
NKT Valpha14 (Mouse)-2C12 TCR: C
NKT Vbeta8.2 (Mouse)-2C12 TCR: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

NKT Valpha14 (Mouse)-2C12 TCR

NKT Vbeta8.2 (Mouse)-2C12 TCR

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