BMRB Entry 34604

Name: Solution structure of MLKL executioner domain in complex with a fragment
Published: 2021-09-17

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PDB ID: 7nm4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34604
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 MLKL executioner domain in complex with a fragment

Deposition date:

2021-02-23

Original release date:

2021-09-17

Authors:

Ruebbelke, M.; Bauer, M.; Hamilton, J.; Binder, F.; Nar, H.; Zeeb, M.

Citation:

Citation: Ruebbelke, M.; Hamilton, J.; Binder, F.; Bauer, M.; King, J.; Nar, H.; Zeeb, M.. "Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain" J. Med. Chem. 64, 15629-15638 (2021).
PubMed: 34672548

Assembly members:

Assembly members:
entity_1, polymer, 157 residues, 18184.961 Da.
entity_UJ8, non-polymer, 266.338 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSPGENLKHIITLGQVIHKR CEEMKYCKKQCRRLGHRVLG LIKPLEMLQDQGKRSVPSEK LTTAMNRFKAALEEANGEIE KFSNRSNICRFLTASQDKIL FKDVNRKLSDVWKELSLLLQ VEQRMPVSPISQGASWAQED QQDADEDRRAFQMLRRD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	511
15N chemical shifts	159
1H chemical shifts	1061

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_1 157 residues - 18184.961 Da.

1

GLY

SER

PRO

GLY

GLU

ASN

LEU

LYS

HIS

ILE

2

ILE

THR

LEU

GLY

GLN

VAL

ILE

HIS

LYS

ARG

3

CYS

GLU

MET

LYS

TYR

CYS

LYS

GLN

4

CYS

ARG

LEU

GLY

HIS

ARG

VAL

LEU

GLY

5

LEU

ILE

LYS

PRO

LEU

GLU

MET

LEU

GLN

ASP

6

GLN

GLY

LYS

ARG

SER

VAL

PRO

SER

GLU

LYS

7

LEU

THR

ALA

MET

ASN

ARG

PHE

LYS

ALA

8

ALA

LEU

GLU

ALA

ASN

GLY

GLU

ILE

GLU

9

LYS

PHE

SER

ASN

ARG

SER

ASN

ILE

CYS

ARG

10

PHE

LEU

THR

ALA

SER

GLN

ASP

LYS

ILE

LEU

11

PHE

LYS

ASP

VAL

ASN

ARG

LYS

LEU

SER

ASP

12

VAL

TRP

LYS

GLU

LEU

SER

LEU

GLN

13

VAL

GLU

GLN

ARG

MET

PRO

VAL

SER

PRO

ILE

14

SER

GLN

GLY

ALA

SER

TRP

ALA

GLN

GLU

ASP

15

GLN

ASP

ALA

ASP

GLU

ASP

ARG

ALA

16

PHE

GLN

MET

LEU

ARG

ASP

Entity 2, unit_2 - C17 H18 N2 O - 266.338 Da.

1

UJ8

Samples:

sample_1: MLKL executioner domain, [U-13C; U-15N], 385 uM; Cpd 3 2000 uM

sample_2: MLKL executioner domain, [U-13C; U-15N], 315 uM; Cpd 3 1600 uM

sample_conditions_1: ionic strength: 170 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 170 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D HNCACB	sample_2	isotropic	sample_conditions_2
3D HNccH TOCSY	sample_2	isotropic	sample_conditions_2
3D HNCC TOCSY	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D filt. 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.98.9, Guntert, Mumenthaler and Wuthrich - structure calculation

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

TopSpin v3.5, Bruker Biospin - processing

TopSpin v3.6, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III HD 600 MHz

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