BMRB Entry 35025

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR35025
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
Solution structure of thanatin in complex with LptDm
Deposition date:
2025-10-28
Original release date:
2026-06-16
Authors:
Schuster, M.; Zerbe, O.
Citation:

Citation: Dai, Wenzhao; Hu, Wenxuan; Schuster, Matthias; Rozic, Laetitia; Roschitzki, Bernd; Zerbe, Oliver. "Computational design of a soluble mimic of the outer membrane LPS transport protein LptD suitable for screening of antibiotics"  Protein Sci. 35, e70626-e70626 (2026).
PubMed: 42144870

Assembly members:

Assembly members:
entity_1, polymer, 181 residues, 19317.424 Da.
entity_2, polymer, 21 residues, 2441.984 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GDTNDLPVTINADHAKGDYP DDAVFTGSVDIMQGNSRLQA DEVQLHQKEAPGQPEPVRTV DALGNVHYDDNQVILKGPKG WANLNTKDWVFYDASIETVG APGSASAKVIKSLDNGKTLE FDDATFDSYENAEALIEHAI KTMGVKTITINNATGAITAE KATKLKAKAAELGATLTITL K
entity_2: GSKKPVPIIYCNRRTGKCQR M

Data sets:
Data typeCount
13C chemical shifts745
15N chemical shifts185
1H chemical shifts1348

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 181 residues - 19317.424 Da.

1   GLYASPTHRASNASPLEUPROVALTHRILE
2   ASNALAASPHISALALYSGLYASPTYRPRO
3   ASPASPALAVALPHETHRGLYSERVALASP
4   ILEMETGLNGLYASNSERARGLEUGLNALA
5   ASPGLUVALGLNLEUHISGLNLYSGLUALA
6   PROGLYGLNPROGLUPROVALARGTHRVAL
7   ASPALALEUGLYASNVALHISTYRASPASP
8   ASNGLNVALILELEULYSGLYPROLYSGLY
9   TRPALAASNLEUASNTHRLYSASPTRPVAL
10   PHETYRASPALASERILEGLUTHRVALGLY
11   ALAPROGLYSERALASERALALYSVALILE
12   LYSSERLEUASPASNGLYLYSTHRLEUGLU
13   PHEASPASPALATHRPHEASPSERTYRGLU
14   ASNALAGLUALALEUILEGLUHISALAILE
15   LYSTHRMETGLYVALLYSTHRILETHRILE
16   ASNASNALATHRGLYALAILETHRALAGLU
17   LYSALATHRLYSLEULYSALALYSALAALA
18   GLULEUGLYALATHRLEUTHRILETHRLEU
19   LYS

Entity 2, unit_2 21 residues - 2441.984 Da.

1   GLYSERLYSLYSPROVALPROILEILETYR
2   CYSASNARGARGTHRGLYLYSCYSGLNARG
3   MET

Samples:

sample_1: LptDm, [U-13C; U-15N], 1 mM; thanatin 1.5 mM; Na-Phosphate 20 mM; NaCl 150 mM

sample_2: LptDm, [U-13C; U-15N; U-2H], 600 uM; thanatin 540 uM; Na-Phosphate 20 mM; NaCl 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1

Software:

Amber vAmber19, OpenMM - refinement

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - structure calculation

CcpNmr Analysis v3.2, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE NEO 700 MHz
  • Bruker AVANCE NEO 600 MHz
  • Bruker AVANCE III 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks