BMRB Entry 52600

Name: chemical shift assignments of a De novo design of protein that bind naphthalenediimides
Published: 2025-03-06

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PDB ID: 9dm3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52600
MolProbity Validation Chart

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NMR-STAR v3 text file.
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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:

chemical shift assignments of a De novo design of protein that bind naphthalenediimides

Deposition date:

2024-09-10

Original release date:

2025-03-06

Authors:

Mann, Samuel; Wu, Yibing; Kelly, Mark; Degrado, William

Citation:

Citation: Mann, Samuel; Lin, Zhi; Tan, Sophia; Zhu, Jiaqi; Widel, Zachary; Bakanas, Ian; Mansergh, Jarrett; Liu, Rui; Kelly, Mark; Wu, Yibing; Wells, James; Therien, Michael; DeGrado, William. "De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties" J. Am. Chem. Soc. 147, 7849-7858 (2025).
PubMed: 39982408

Assembly members:

Assembly members:
entity_1, polymer, 132 residues, Formula weight is not available

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 Vector: BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: HHHHHHENLYFQSSAKQDFA EGVKLWQENAVLWTRLVQAF QSGDQSTVDSLLKQLDANAA RVEQLLQRIISETGDELARK GESLFQRNQQLFSQLKTLFS QGDEDTAKAVLEEIQSNLNQ IQQIITEAQKRL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	451
15N chemical shifts	165
1H chemical shifts	983

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protein	1

Entities:

Entity 1, protein 132 residues - Formula weight is not available

1

HIS

GLU

ASN

LEU

TYR

2

PHE

GLN

SER

ALA

LYS

GLN

ASP

PHE

ALA

3

GLU

GLY

VAL

LYS

LEU

TRP

GLN

GLU

ASN

ALA

4

VAL

LEU

TRP

THR

ARG

LEU

VAL

GLN

ALA

PHE

5

GLN

SER

GLY

ASP

GLN

SER

THR

VAL

ASP

SER

6

LEU

LYS

GLN

LEU

ASP

ALA

ASN

ALA

7

ARG

VAL

GLU

GLN

LEU

GLN

ARG

ILE

8

SER

GLU

THR

GLY

ASP

GLU

LEU

ALA

ARG

LYS

9

GLY

GLU

SER

LEU

PHE

GLN

ARG

ASN

GLN

10

LEU

PHE

SER

GLN

LEU

LYS

THR

LEU

PHE

SER

11

GLN

GLY

ASP

GLU

ASP

THR

ALA

LYS

ALA

VAL

12

LEU

GLU

ILE

GLN

SER

ASN

LEU

ASN

GLN

13

ILE

GLN

ILE

THR

GLU

ALA

GLN

LYS

14

ARG

LEU

Samples:

sample_1: protein, [U-100% 13C; U-100% 15N], 0.2 M; Naphthalenediimide 0.2 M

sample_conditions_1: ionic strength: 200 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCANH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
F1_F2_fil_TOCSY	sample_1	isotropic	sample_conditions_1
F1_fil_NOESY	sample_1	isotropic	sample_conditions_1
3D NOESY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN - collection

NMR spectrometers:

Bruker Avance 800 MHz

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