BMRB Entry 34716

Name: Solution structure of thanatin-like derivative 7 in complex with K. pneumoniae LptA
Published: 2023-05-30

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PDB ID: 7zax
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34716
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of thanatin-like derivative 7 in complex with K. pneumoniae LptA

Deposition date:

2022-03-22

Original release date:

2023-05-30

Authors:

Oi, K.; Moehle, K.; Zerbe, O.

Citation:

Citation: Schuster, M.; Brabet, E.; Oi, K.; Desjonqueres, N.; Moehle, K.; Le Poupon, K.; Hell, S.; Gable, S.; Rithie, V.; Dillinger, S.; Zbinden, P.; Luther, A.; Li, C.; Stiegeler, S.; D'Arco, C.; Locher, H.; Remus, T.; DiMaio, S.; Motta, P.; Wach, A.; Jung, F.; Upert, G.; Obrecht, D.; Benghezal, M.; Zerbe, O.. "Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae." Sci. Adv. 9, eadg3683-eadg3683 (2023).
PubMed: 37224246

Assembly members:

Assembly members:
entity_1, polymer, 133 residues, 14790.585 Da.
entity_2, polymer, 16 residues, 2007.387 Da.

Natural source:

Natural source: Common Name: Klebsiella pneumoniae Taxonomy ID: 573 Superkingdom: Bacteria Kingdom: not available Genus/species: Klebsiella pneumoniae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli K-12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GKTGDTDQPIHIESDQQSLD MQGNVVTFTGNVVVTQGTIK INADKVVVTRPGNEKGKEVI EGFGNPATFYQMQDNGKPVK GRASKMRYELQNDYVVLTGN AYLEQLDSNIKGDKITYLVK EQKMQAFSDKGRR
entity_2: XXITYXNRXTXKCXRY

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	552
15N chemical shifts	143
1H chemical shifts	1018

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 133 residues - 14790.585 Da.

1

GLY

LYS

THR

GLY

ASP

THR

ASP

GLN

PRO

ILE

2

HIS

ILE

GLU

SER

ASP

GLN

SER

LEU

ASP

3

MET

GLN

GLY

ASN

VAL

THR

PHE

THR

GLY

4

ASN

VAL

THR

GLN

GLY

THR

ILE

LYS

5

ILE

ASN

ALA

ASP

LYS

VAL

THR

ARG

6

PRO

GLY

ASN

GLU

LYS

GLY

LYS

GLU

VAL

ILE

7

GLU

GLY

PHE

GLY

ASN

PRO

ALA

THR

PHE

TYR

8

GLN

MET

GLN

ASP

ASN

GLY

LYS

PRO

VAL

LYS

9

GLY

ARG

ALA

SER

LYS

MET

ARG

TYR

GLU

LEU

10

GLN

ASN

ASP

TYR

VAL

LEU

THR

GLY

ASN

11

ALA

TYR

LEU

GLU

GLN

LEU

ASP

SER

ASN

ILE

12

LYS

GLY

ASP

LYS

ILE

THR

TYR

LEU

VAL

LYS

13

GLU

GLN

LYS

MET

GLN

ALA

PHE

SER

ASP

LYS

14

GLY

ARG

Entity 2, unit_2 16 residues - 2007.387 Da.

1

EU0

HYP

ILE

THR

TYR

LE1

ASN

ARG

DAB

THR

2

4FO

LYS

CYS

DAB

ARG

TYR

Samples:

sample_1: Lipopolysaccharide export system protein LptA, [U-13C; U-15N], 300 ± 10 uM; sodium phosphate, none, 50 mM; NaCl, none, 150 mM; Thanatin-like derivative 4, none, 500 uM

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

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

MOE v2020.09, Chemical Computing Group ULC, 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2022 - refinement

CARA, Keller and Wuthrich - chemical shift assignment

CcpNmr Analysis, CCPN - peak picking

NMR spectrometers:

Bruker AVANCE NEO 700 MHz
Bruker AVANCE NEO 600 MHz

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