BMRB Entry 36621

Name: Structure of LL-D49194-alpha-1 covalently bound to guanosine-2&#039;-fluorinated d(AACCGGTT)2
Published: 2025-12-15

Click here to enlarge.

PDB ID: 8xc7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36621
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of LL-D49194-alpha-1 covalently bound to guanosine-2'-fluorinated d(AACCGGTT)2

Deposition date:

2023-12-08

Original release date:

2025-12-15

Authors:

Gao, R.; Tang, G.; Cao, C.

Citation:

Citation: Gao, Ruo-Qin; Hu, Xiao-Dong; Zhou, Qiang; Hou, Xian-Feng; Cao, Chunyang; Tang, Gong-Li. "Different DNA Binding and Damage Mode between Anticancer Antibiotics Trioxacarcin A and LL-D49194a1." JACS Au. 4, 3641-3648 (2024).
PubMed: 39328742

Assembly members:

Assembly members:
DNA (5'-D(*AP*AP*CP*CP*2''F-GP*2''F-GP*TP*T)-3'), polymer, 8 residues, 2382.619 Da.
LL-D49194alpha1, non-polymer, 995.024 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 2853804 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*AP*AP*CP*CP*2''F-GP*2''F-GP*TP*T)-3'): XACCXXTT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	98

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1_1	1
2	entity_1_2	1
3	entity_A1LVV	2

Entities:

Entity 1, entity_1_1 8 residues - 2382.619 Da.

1

3D1

DA

DC

GF2

DT

Entity 2, entity_A1LVV - C48 H66 O22 - 995.024 Da.

1

A1LVV

Samples:

sample_1: DNA-LLD 2 mM; sodium chloride 20 mM; sodium phosphate 10 mM; H2O 90.0%; D2O, [U-2H], 10.0%

sample_conditions_1: ionic strength: 44.4 mM; pH: 7.2; pressure: 1 atm; temperature: 293 K

Experiments:

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

Software:

NMRFAM-SPARKY, Woonghee Lee,* Marco Tonelli, and John L. Markley* - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

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

NMRFAM-SPARKY, Woonghee Lee,* Marco Tonelli, and John L. Markley* - peak picking

NMRFAM-SPARKY, Woonghee Lee,* Marco Tonelli, and John L. Markley* - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker AVANCE 850 MHz