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PDB ID: 6llq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36305
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Name: Solution NMR structure of de novo Rossmann2x2 fold with almost valines in the core, R2x2_VAL88
Published: 2026-03-26

Title:

Solution NMR structure of de novo Rossmann2x2 fold with almost valines in the core, R2x2_VAL88

Deposition date:

2019-12-23

Original release date:

2026-03-26

Authors:

Kobayashi, N.; Sugiki, T.; Fujiwara, T.; Koga, R.; Yamamoto, M.; Kosugi, T.; Koga, N.

Citation:

Citation: Koga, Rie; Yamamoto, Mami; Kosugi, Takahiro; Kobayashi, Naohiro; Sugiki, Toshihiko; Fujiwara, Toshimichi; Koga, Nobuyasu. "Robust folding of a de novo designed ideal protein even with most of the core mutated to valine." Proc. Natl. Acad. Sci. U. S. A. 117, 31149-31156 (2020).
PubMed: 33229587

Assembly members:

Assembly members:
VAL88, polymer, 98 residues, 11105.688 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32644 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VAL88: GRVVVVVTSEQVKEEVRKKF PQVEVRVVTTEEDAKQVVKE VQKKGVQKVVVVGVSEKVVQ KVKQEANVQVYRVTSNDEVE QVVKDVKGSGLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	403
15N chemical shifts	96
1H chemical shifts	624

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 98 residues - 11105.688 Da.

1

GLY

ARG

VAL

THR

SER

GLU

2

GLN

VAL

LYS

GLU

VAL

ARG

LYS

PHE

3

PRO

GLN

VAL

GLU

VAL

ARG

VAL

THR

4

GLU

ASP

ALA

LYS

GLN

VAL

LYS

GLU

5

VAL

GLN

LYS

GLY

VAL

GLN

LYS

VAL

6

VAL

GLY

VAL

SER

GLU

LYS

VAL

GLN

7

LYS

VAL

LYS

GLN

GLU

ALA

ASN

VAL

GLN

VAL

8

TYR

ARG

VAL

THR

SER

ASN

ASP

GLU

VAL

GLU

9

GLN

VAL

LYS

ASP

VAL

LYS

GLY

SER

GLY

10

LEU

GLU

HIS

Samples:

sample_1: VAL88, [U-99% 13C; U-99% 15N], 500 uM; sodium chloride 100 mM; potassium phosphate 7.4 mM; sodium phosphate 1.2 mM; D2O, [U-2H], 5%; H2O 95%

sample_2: VAL88, [U-99% 13C; U-99% 15N], 100 uM; Pf1 phage 10 mg/mL; sodium chloride 100 mM; potassium phosphate 7.4 mM; sodium phosphate 1.2 mM; D2O, [U-2H], 5%; H2O 95%

sample_conditions_1: ionic strength: 108.6 mM; pH: 6.0; pressure: 1.0 atm; temperature: 303 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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	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
2D 1H-15N IPAP HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_2	anisotropic	sample_conditions_1
3D HCCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v9.0, Johnson, One Moon Scientific - chemical shift assignment

MAGRO v2.0.24, Kobayashi, N. - data analysis

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

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

TALOS vTALOS+, Yang, S. and Bax, Ad. - data analysis

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - refinement

MAGRO v2.01.12, Kobayashi, N. upgraded version of Kujira (Kobayshi, N. et al., 2007) - data analysis

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 950 MHz

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

BMRB Entry 36305