SMTL ID : 9lsi.1

Cryo-EM structure of the S82C-S82C diabody complex (CitS-diabody #2-TLR3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

3 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: 4 residues within 4Å: Chain E: K.200, N.252, M.278, Y.302 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain E: N.291, F.314, S.315, H.316, D.347 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain E: N.507, K.531 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.3: 4 residues within 4Å: Chain E: E.363, S.387, N.413, D.437 No protein-ligand interaction detected (PLIP)

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 8 residues within 4Å: Chain A: N.186, G.187, Y.348, R.402, G.403, G.404, S.405, R.428 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.186, A:G.404, A:S.405 Salt bridges: A:R.402, A:R.428

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 8 residues within 4Å: Chain A: F.116, H.265, R.327, F.331 Chain B: I.51, H.265, R.327, F.331 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.51, B:F.331, A:F.116, A:F.331 Salt bridges: B:H.265, A:H.265, A:R.327

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

NAG.7: 2 residues within 4Å: Chain E: P.50, N.52 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.52 NAG.8: 4 residues within 4Å: Chain E: P.99, M.100, K.102, N.124 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.124 NAG.9: 4 residues within 4Å: Chain E: N.265, T.266, N.291, D.292 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:N.291 Hydrogen bonds: E:N.265, E:D.292 NAG.10: 4 residues within 4Å: Chain E: T.248, S.249, T.274, N.275 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.248, E:N.275 NAG.11: 2 residues within 4Å: Chain E: N.398, E.399 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Disulfide-stabilized diabodies enable near-atomic cryo-EM imaging of small proteins: A case study of the bacterial Na + /citrate symporter CitS. Structure (2025)

Release Date

2025-03-12

Peptides

Citrate/sodium symporter: AB
Diabody (CitS VH-TLR3 VL): C
Diabody (TLR3 VH-CitS VL): D
Toll-like receptor 3: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Citrate/sodium symporter

Diabody (CitS VH-TLR3 VL)

Diabody (TLR3 VH-CitS VL)

Toll-like receptor 3

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