BMRB Entry 17185

Name: Determination of the Binding Specificity of the Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3
Published: 2010-11-10

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17185

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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:

Determination of the Binding Specificity of the Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3

Deposition date:

2010-09-10

Original release date:

2010-11-10

Authors:

Meinecke, Robert; Meyer, Bernd

Citation:

Citation: Meinecke, Robert; Meyer, Bernd. "Determination of the Binding Specificity of an Integral Membrane Protein by Saturation Transfer Difference NMR: RGD Peptide Ligands Binding to Integrin alphaIIbBeta3" J. Med. Chem. 44, 3059-3065 (2001).
PubMed: 11543674

Assembly members:

Assembly members:
cyclo, polymer, 5 residues, Formula weight is not available
alphaIIb, polymer, 42 residues, Formula weight is not available
beta3, polymer, 43 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
cyclo: RGDXV
alphaIIb: GALEERAIPIWWVLVGVLGG LLLLTILVLAMWKVGFFKRN RP
beta3: PESPKGPDILVVLLSVMGAI LLIGLAALLIWKLLITIHDR KEF

Data sets:

binding constants

Data type	Count
binding constants	6

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cyclo	1
2	alphaIIb	2
3	beta3	3

Entities:

Entity 1, cyclo 5 residues - Formula weight is not available

1

ARG

GLY

ASP

DPN

VAL

Entity 2, alphaIIb 42 residues - Formula weight is not available

1

GLY

ALA

LEU

GLU

ARG

ALA

ILE

PRO

ILE

2

TRP

VAL

LEU

VAL

GLY

VAL

LEU

GLY

3

LEU

THR

ILE

LEU

VAL

LEU

ALA

4

MET

TRP

LYS

VAL

GLY

PHE

LYS

ARG

ASN

5

ARG

PRO

Entity 3, beta3 43 residues - Formula weight is not available

1

PRO

GLU

SER

PRO

LYS

GLY

PRO

ASP

ILE

LEU

2

VAL

LEU

SER

VAL

MET

GLY

ALA

ILE

3

LEU

ILE

GLY

LEU

ALA

LEU

ILE

4

TRP

LYS

LEU

ILE

THR

ILE

HIS

ASP

ARG

5

LYS

GLU

PHE

Samples:

sample_1: cyclo0 – 275 uM; alphaIIb 5 uM; beta3 5 uM; TRIS 10 mM; sodium chloride 10 mM; sodium azide 6 mM; calcium chloride 20.5 mM; D2O 99.9%

sample_2: RGD 274 mM; cyclo 264 mM; alphaIIb 5 uM; beta3 5 uM; TRIS 10 mM; sodium chloride 10 mM; sodium azide 6 mM; calcium chloride 20.5 mM; D2O 99.9%

sample_3: RGD 274 mM; cyclo 264 mM; alphaIIb 5 uM; beta3 5 uM; RGDS 264 mM; TRIS 10 mM; sodium azide 6 mM; sodium chloride 10 mM; calcium chloride 20.5 mM; D2O 99.9%

sample_conditions_1: pD: 7.4; pressure: ambient atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
STD NMR	sample_1	isotropic	sample_conditions_1
STD NMR	sample_2	isotropic	sample_conditions_1
STD NMR	sample_3	isotropic	sample_conditions_1

Software:

xwinnmr v2.5, Bruker Biospin - processing

NMR spectrometers:

Bruker Avance 500 MHz

BMRB	16496 16497 16496 16497
PDB	2K1A 2K9J 2KNC 2K9J 2KNC 2RMZ 2RN0
DBJ	BAG37735 BAI46167 BAG62151 BAJ17755
EMBL	CAA29987
GB	AAA35926 AAA52597 AAA53150 AAA60114 AAA65936 AAA35927 AAA36121 AAA52589 AAA52600 AAA60122
PRF	1403305A
REF	NP_000410 XP_001114526 XP_001150497 XP_002827479 XP_003282434 NP_000203 XP_002748172 XP_002834363 XP_003270746 XP_004041501
SP	P08514 P53711 P05106
AlphaFold	P53711 P08514 P05106