BMRB Entry 52792

Name: t44 VEGF aptamer in VEGF HBD bound form
Published: 2025-11-19

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52792

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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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Title:

t44 VEGF aptamer in VEGF HBD bound form

Deposition date:

2025-01-03

Original release date:

2025-11-19

Authors:

Takeuchi, Koh; Imai, Misaki; Shimada, Ichio

Citation:

Citation: Takeuchi, Koh; Ueda, Takumi; Imai, Misaki; Fujisaki, Miwa; Tsujimura, Masanari; Tokunaga, Yuji; Kofuku, Yutaka; Shimada, Ichio. "Two-step target recognition for the competitive inhibition activity of an anti-VEGF aptamer" RNA 31, 1368-1378 (2025).
PubMed: 40744710

Assembly members:

Assembly members:
entity_1, polymer, 28 residues, Formula weight is not available
entity_2, polymer, 55 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):
entity_1: XXXAAXXXXXXXXXXXXXXX XXXXXXXX
entity_2: ARQENPCGPCSERRKHLFVQ DPQTCKCSCKNTDSRCKARQ LELNERTCRCDKPRR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	198

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	t44 VEGF aptamer	1
2	VEGF HBD	2

Entities:

Entity 1, t44 VEGF aptamer 28 residues - Formula weight is not available

Bases 1-3 and 6-28 are non-natural nucleotides. The linkage between bases 27 and 28 is a 3'-3' terminal linkage. UFT: 6,10,14,17,18,20,24 CFZ: 1,7,16,22,25,26 A39: 8,12,13,19,21,23 OMG: 2,3,9,11,15,27 THM:28

1

CFZ

OMG

A

UFT

CFZ

A39

OMG

UFT

2

OMG

A39

UFT

OMG

CFZ

UFT

A39

UFT

3

A39

CFZ

A39

UFT

CFZ

OMG

HTM

Entity 2, VEGF HBD 55 residues - Formula weight is not available

VEGF HBD 165, corresponding to nucleotides 111-165 of HBD 165.

1

ALA

ARG

GLN

GLU

ASN

PRO

CYS

GLY

PRO

CYS

2

SER

GLU

ARG

LYS

HIS

LEU

PHE

VAL

GLN

3

ASP

PRO

GLN

THR

CYS

LYS

CYS

SER

CYS

LYS

4

ASN

THR

ASP

SER

ARG

CYS

LYS

ALA

ARG

GLN

5

LEU

GLU

LEU

ASN

GLU

ARG

THR

CYS

ARG

CYS

6

ASP

LYS

PRO

ARG

Samples:

sample_1: t44-27-FL 450 uM; H2O 93%; D2O 7%; TrisHCl 10 mM; CaCl2 2 mM; VEGF-HBD 500 uM

sample_conditions_1: ionic strength: 50 mM; pH: 7.6; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

NMRFAM-SPARKY - chemical shift assignment

TOPSPIN - collection, processing

NMR spectrometers:

Bruker AVANCE III 600 MHz