BMRBj - BMREntryMaster

Found 1 Document (0.379 seconds)

BMRB: 30924

5LJ3

Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer B

Authors

Dickerhoff, J., Yang, D.

Assembly

Myc2345 T23

Entity

1. Myc2345 T23, entity 1 (polymer, Thiol state: not present), 22 monomers, 7096.493 Da Detail

TGAGGGTGGG TAGGGTGGGG AA

2. Myc2345 T23, entity BER (non-polymer), 336.361 × 2 Da

Total weight

7769.2153 Da

Max. entity weight

7096.493 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	97.0 % (196 of 202)	97.0 % (196 of 202)
Suger, PO4	100.0 % (154 of 154)	100.0 % (154 of 154)
Nucleobase	87.5 % (42 of 48)	87.5 % (42 of 48)
Aromatic	86.4 % (38 of 44)	86.4 % (38 of 44)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. entity 1

TGAGGGTGGG TAGGGTGGGG AA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1.2 mM DNA, 3.6 mM Berberine, 10 mM potassium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DNA	natural abundance	1.2 mM
2	Berberine	natural abundance	3.6 mM
3	potassium phosphate	natural abundance	10 mM

Release date

2021-07-01

Citation

Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution
Dickerhoff, J., Brundridge, N., McLuckey, S.A., Yang, D.
J. Med. Chem. (2021), 64, 16205-16212, PubMed 34677968 , DOI 10.1021/acs.jmedchem.1c01508 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30923 released on 2021-07-01
Title Solution structure of the MYC promoter G-quadruplex in complex with berberine: conformer A

Related entities 1. Myc2345 T23, entity 1, : 1 : 22 entities Detail

Experiments performed 3 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30924_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
2	1	BER	BERBERINE	Assigned chemical shifts

Content subtype: bmr30924_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	249		100.0 (chain: 2, length: 1), 100.0 (chain: 1, length: 22)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 2, Chain length: 1, Sequence coverage: 100.0%
- Entity_assembly_ID: 1, Chain length: 22, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 222
- ¹³C chemical shifts: 27

Completeness of assignments

Entity_assemble_ID: 2

Comp_index_ID	Comp_ID
1	BER

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DT	C6	139.788
2	DG	C8	139.21
3	DA	C2	155.348
3	DA	C8	142.284
4	DG	C8	138.788
5	DG	C8	137.826
6	DG	C8	138.002
7	DT	C6	140.265
8	DG	C8	138.122
9	DG	C8	138.429
10	DG	C8	138.133
11	DT	C6	140.453
12	DA	C2	155.959
12	DA	C8	143.806
13	DG	C8	138.469
14	DG	C8	138.104
15	DG	C8	138.207
16	DT	C6	140.265
17	DG	C8	138.076
18	DG	C8	138.519
19	DG	C8	137.45
20	DG	C8	139.894
21	DA	C2	154.994
21	DA	C8	141.92
22	DA	C2	155.092
22	DA	C8	142.108

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	202	196	97.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	154	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	42	87.5

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0

Histogram of normalized assigned chemical shifts

Keywords BERBERINE, CANCER, DNA, DRUG-DNA COMPLEX, G-QUADRUPLEX DNA

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Found 1 Document (0.379 seconds)

BMRB: 30924

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Myc2345 T23, entity 1, : 1 : 22 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail