BMRB Entry 34240

Name: Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants
Published: 2019-03-28

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PDB ID: 6fvc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR34240
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:

Protein environment affects the water-tryptophan binding mode. Molecular dynamics simulations of Engrailed homeodomain mutants

Deposition date:

2018-03-02

Original release date:

2019-03-28

Authors:

Trosanova, Z.; Zachrdla, M.; Jansen, S.; Srb, P.; Zidek, L.; Kozelka, J.

Citation:

Citation: Spackova, N.; Trosanova, Z.; Sebesta, F.; Jansen, S.; Burda, J.; Srb, P.; Zachrdla, M.; Zidek, L.; Kozelka, J.. "Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants." Phys. Chem. Chem. Phys. 20, 12664-12677 (2018).
PubMed: 29696277

Assembly members:

Assembly members:
entity_1, polymer, 64 residues, 7626.657 Da.
entity_HOH, water, 18.015 Da.

Natural source:

Natural source: Common Name: Fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMEKRPRTAFSSEQLARLK REFNENRYLTERRRQQLSSE LGLNEAQIKIWFQNERAKIK KSGS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	466

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 64 residues - 7626.657 Da.

1

GLY

ALA

MET

GLU

LYS

ARG

PRO

ARG

THR

ALA

2

PHE

SER

GLU

GLN

LEU

ALA

ARG

LEU

LYS

3

ARG

GLU

PHE

ASN

GLU

ASN

ARG

TYR

LEU

THR

4

GLU

ARG

GLN

LEU

SER

GLU

5

LEU

GLY

LEU

ASN

GLU

ALA

GLN

ILE

LYS

ILE

6

TRP

PHE

GLN

ASN

GLU

ARG

ALA

LYS

ILE

LYS

7

LYS

SER

GLY

SER

Entity 2, entity_2 - 18.015 Da.

1

HOH

Samples:

sample_1: EnHD_K52E 1 mM

sample_conditions_1: ionic strength: 150 mM; pH: 5.7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AvanceIII 850 MHz