SMTL ID : 9lsh.1

Cryo-EM structure of the wild-type diabody complex (CitS-diabody #1-TLR3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-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: 4 residues within 4Å: Chain C: K.200, N.252, M.278, Y.302 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.302 NAG-NAG.2: 5 residues within 4Å: Chain C: N.291, F.314, S.315, H.316, D.347 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: 3 residues within 4Å: Chain C: Y.383, N.413, D.437 No protein-ligand interaction detected (PLIP)

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

CIT.4: 2 residues within 4Å: Chain A: G.187, A.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.187, A:G.187 Salt bridges: A:H.299

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 7 residues within 4Å: Chain A: I.51, S.114, F.116, H.265, F.331 Chain B: I.51, F.331 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.51, B:F.331, A:I.51, A:F.116, A:F.331 Salt bridges: A:H.265

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

NAG.6: 2 residues within 4Å: Chain C: P.50, N.52 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.52 NAG.7: 4 residues within 4Å: Chain C: P.99, M.100, N.124, N.148 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain C: R.251, W.273, T.274, N.275 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.275 NAG.9: 2 residues within 4Å: Chain C: N.398, E.399 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.398 NAG.10: 4 residues within 4Å: Chain C: R.506, N.507, E.530, K.531 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
Toll-like receptor 3: C
Diabody (CitS VH-TLR3 VL): D
Diabody (TLR3 VH-CitS VL): 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

Toll-like receptor 3

Diabody (CitS VH-TLR3 VL)

Diabody (TLR3 VH-CitS VL)

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