BMRB Entry 50285

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50285

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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:

Backbone and methyl chemical shift assignments, relaxation data and order parameters of Galectin-3C in complex with ortho-fluoroaryltriazole galactopyranosyl 1-thio-D-glucopyranoside derivative

Deposition date:

2020-05-20

Original release date:

2020-12-02

Authors:

Wallerstein, Johan; Misini Ignjatovic, Majda; Kumar, Rohit; Caldararu, Octav; Peterson, Kristoffer; Leffler, Hakon; Logan, Derek; Nilsson, Ulf; Ryde, Ulf; Akke, Mikael

Citation:

Citation: Wallerstein, Johan; Ekberg, Vilhelm; Misini Ignjatovic, Majda; Kumar, Rohit; Caldararu, Octav; Peterson, Kristoffer; Wernersson, Sven; Brath, Ulrika; Leffler, Hakon; Oksanen, Esko; Logan, Derek; Nilsson, Ulf; Ryde, Ulf; Akke, Mikael. "Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C" JACS Au. 1, 484-500 (2021).

Assembly members:

Assembly members:
entity_1, polymer, . residues, Formula weight is not available
entity_KP5, non-polymer, 503.499 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 Vector: pLysS pGal3CRD

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: PLIVPYNLPLPGGVVPRMLI TILGTVKPNANRIALDFQRG NDVAFHFNPRFNENNRRVIV CNTKLDNNWGREERQSVFPF ESGKPFKIQVLVEPDHFKVA VNDAHLLQYNHRVKKLNEIS KLGISGDIDLTSASYTMI

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2
heteronucl_NOEs
heteronucl_T1_relaxation
heteronucl_T2_relaxation
order_parameters
- order_parameters_1
- order_parameters_2

Data type	Count
13C chemical shifts	85
15N chemical shifts	122
1H chemical shifts	377
T1 relaxation values	366
T2 relaxation values	366
heteronuclear NOE values	366
order parameters	189

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	gal3C	1
2	ligand O	2

Entities:

Entity 1, gal3C - Formula weight is not available

1

PRO

LEU

ILE

VAL

PRO

TYR

ASN

LEU

PRO

LEU

2

PRO

GLY

VAL

PRO

ARG

MET

LEU

ILE

3

THR

ILE

LEU

GLY

THR

VAL

LYS

PRO

ASN

ALA

4

ASN

ARG

ILE

ALA

LEU

ASP

PHE

GLN

ARG

GLY

5

ASN

ASP

VAL

ALA

PHE

HIS

PHE

ASN

PRO

ARG

6

PHE

ASN

GLU

ASN

ARG

VAL

ILE

VAL

7

CYS

ASN

THR

LYS

LEU

ASP

ASN

TRP

GLY

8

ARG

GLU

ARG

GLN

SER

VAL

PHE

PRO

PHE

9

GLU

SER

GLY

LYS

PRO

PHE

LYS

ILE

GLN

VAL

10

LEU

VAL

GLU

PRO

ASP

HIS

PHE

LYS

VAL

ALA

11

VAL

ASN

ASP

ALA

HIS

LEU

GLN

TYR

ASN

12

HIS

ARG

VAL

LYS

LEU

ASN

GLU

ILE

SER

13

LYS

LEU

GLY

ILE

SER

GLY

ASP

ILE

ASP

LEU

14

THR

SER

ALA

SER

TYR

THR

MET

ILE

Entity 2, ligand O - C20 H26 F N3 O9 S - 503.499 Da.

1

KP5

Samples:

sample_1: Galectin-3C, [U-100% 15N], 0.85 mM; ligand O 0.83 ± 0.06 mM; HEPES 5 mM; D2O, [U-2H], 10%

sample_2: Galectin-3C, [U-100% 13C; U-100% 15N], 0.85 mM; ligand M 0.83 ± 0.06 mM; HEPES 5 mM; D2O, [U-2H], 10%

sample_3: Galectin-3C, [U-100% 13C; U-100% 15N; U-60% 2H], 0.85 mM; ligand O 0.83 ± 0.06 mM; HEPES 5 mM; D2O, [U-2H], 10%

sample_conditions_1: pH: 7.4; temperature: 301 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation 500	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation 600	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation 800	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation 500	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation 600	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation 800	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
1H-15N heteronoe 500	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe 600	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe 800	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
R1(Dz)_methyl 500	sample_3	isotropic	sample_conditions_1
R1(Dz)_methyl 600	sample_3	isotropic	sample_conditions_1
R2(D+)_methyl 500	sample_3	isotropic	sample_conditions_1
R2(D+)_methyl 600	sample_3	isotropic	sample_conditions_1
R(3Dz^2-2)_methyl 500	sample_3	isotropic	sample_conditions_1
R(3Dz^2-2)_methyl 600	sample_3	isotropic	sample_conditions_1
R(D+Dz + DzD+)_methyl 500	sample_3	isotropic	sample_conditions_1
R(D+Dz + DzD+)_methyl 600	sample_3	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v2.0 - chemical shift assignment, data analysis, peak picking

Chimera v1.13 - data analysis, geometry optimization

NMRPipe - data analysis, processing

NMRDraw - data analysis

PiNT v2.1.0 - chemical shift calculation, peak picking

Relax v4.0.320 - data analysis, refinement

Matlab v2018b - data analysis, model-free fitting

NMR spectrometers:

Varian VNMRS 500 MHz
Varian VNMRS 600 MHz
Bruker Avance 800 MHz