SMTL ID : 6nig.2 (1 other biounit)

Crystal structure of the human TLR2-Diprovocim complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

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: 9 residues within 4Å: Chain A: R.395, S.421, K.422, Y.440, N.442, S.444, I.461, D.463, Y.483 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.422 NAG-NAG.2: 9 residues within 4Å: Chain B: R.395, S.421, K.422, Y.440, N.442, S.444, I.461, D.463, Y.483 No protein-ligand interaction detected (PLIP)

2 x KQD: (3S,4S,3'S,4'S)-1,1'-(1,4-phenylenedicarbonyl)bis{N~3~,N~4~-bis[(1S,2R)-2-phenylcyclopropyl]pyrrolidine-3,4-dicarboxami de}(Non-covalent)

KQD.3: 36 residues within 4Å: Chain A: L.289, L.312, I.314, I.319, Y.323, F.325, Y.326, D.327, L.328, S.329, L.331, Y.332, T.335, K.347, F.349, L.350, L.355, Y.376 Chain B: L.289, L.312, I.314, I.319, Y.323, F.325, Y.326, D.327, L.328, S.329, L.331, Y.332, T.335, K.347, F.349, L.350, Y.376 Ligands: KQD.5 25 PLIP interactions: 11 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:Y.323, B:Y.326, B:L.331, B:Y.332, B:F.349, B:L.350, A:Y.323, A:F.325, A:Y.326, A:Y.332, A:Y.332, A:T.335, A:F.349, A:L.350 Hydrogen bonds: B:Y.326, B:L.328, B:Y.332, A:Y.326, A:L.328, A:Y.332, A:Y.332 pi-Stacking: B:F.325, B:Y.376, A:F.325, A:Y.376 KQD.5: 43 residues within 4Å: Chain A: L.289, I.314, L.317, I.319, F.325, Y.326, Y.332, I.341, V.343, S.346, K.347, V.348, F.349, L.350, V.351, P.352, L.355, L.359, L.365, L.367 Chain B: L.289, L.312, I.314, L.317, I.319, F.325, Y.326, Y.332, I.341, V.343, S.346, K.347, V.348, F.349, L.350, V.351, P.352, L.355, L.359, L.362, L.365, L.367 Ligands: KQD.3 27 PLIP interactions: 14 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:I.314, A:L.317, A:I.319, A:I.341, A:V.343, A:V.351, A:L.355, A:L.365, A:L.367, B:I.314, B:L.317, B:I.319, B:I.341, B:V.343, B:V.351, B:L.355, B:L.365, B:L.367 Hydrogen bonds: A:Y.332, A:K.347, A:F.349, A:L.350, A:L.350, B:K.347, B:F.349, B:L.350, B:L.350

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

NAG.4: 5 residues within 4Å: Chain A: P.387, S.388, K.413, N.414, K.437 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.387 NAG.6: 4 residues within 4Å: Chain B: F.175, N.199, S.222, L.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.199 NAG.7: 4 residues within 4Å: Chain B: P.387, S.388, N.414, K.437 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, L. et al., Structural Basis of TLR2/TLR1 Activation by the Synthetic Agonist Diprovocim. J. Med. Chem. (2019)

Release Date

2019-04-17

Peptides

Toll-like receptor 2,Variable lymphocyte receptor B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Toll-like receptor 2,Variable lymphocyte receptor B

Related Entries With Identical Sequence