HEADER DNA 03-OCT-20 7KBX
TITLE SOLUTION STRUCTURE OF THE MAJOR MYC PROMOTER G-QUADRUPLEX IN COMPLEX
TITLE 2 WITH NSC85697, A QUINOLINE DERIVATIVE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MYC2345_T23;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_COMMON: HUMAN;
SOURCE 5 ORGANISM_TAXID: 9606
KEYWDS G-QUADRUPLEX DNA, DRUG-DNA COMPLEX, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR J.DICKERHOFF,D.YANG
REVDAT 2 01-MAY-24 7KBX 1 REMARK
REVDAT 1 23-JUN-21 7KBX 0
JRNL AUTH J.DICKERHOFF,J.DAI,D.YANG
JRNL TITL STRUCTURAL RECOGNITION OF THE MYC PROMOTER G-QUADRUPLEX BY A
JRNL TITL 2 QUINOLINE DERIVATIVE: INSIGHTS INTO MOLECULAR TARGETING OF
JRNL TITL 3 PARALLEL G-QUADRUPLEXES.
JRNL REF NUCLEIC ACIDS RES. V. 49 5905 2021
JRNL REFN ESSN 1362-4962
JRNL PMID 33978746
JRNL DOI 10.1093/NAR/GKAB330
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 16, AMBER 16, X-PLOR NIH
REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG,
REMARK 3 DUKE, LUO, AND KOLLMAN (AMBER), CASE, DARDEN,
REMARK 3 CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, AND
REMARK 3 KOLLMAN (AMBER), SCHWIETERS, KUSZEWSKI, TJANDRA
REMARK 3 AND CLORE (X-PLOR NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7KBX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-20.
REMARK 100 THE DEPOSITION ID IS D_1000252210.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 293
REMARK 210 PH : 6.5; 6.5
REMARK 210 IONIC STRENGTH : 10; 10
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.7 MM MYC2345_T23, 2.1 MM
REMARK 210 NSC85697, 10 MM POTASSIUM
REMARK 210 PHOSPHATE, 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES
REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DA A 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES
REMARK 500 1 DA A 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DA A 15 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DT A 19 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DT A 23 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 23 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DA A 24 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DA A 24 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 DA A 24 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DA A 24 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 DA A 25 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA A 25 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 DA A 25 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DA A 25 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 2 DA A 6 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DA A 6 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 2 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DA A 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES
REMARK 500 2 DA A 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DA A 15 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 2 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 307 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 DG A 11 0.05 SIDE CHAIN
REMARK 500 1 DG A 12 0.06 SIDE CHAIN
REMARK 500 1 DG A 13 0.06 SIDE CHAIN
REMARK 500 5 DG A 18 0.08 SIDE CHAIN
REMARK 500 7 DG A 12 0.06 SIDE CHAIN
REMARK 500 9 DG A 7 0.05 SIDE CHAIN
REMARK 500 9 DG A 12 0.06 SIDE CHAIN
REMARK 500 10 DG A 7 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1XAV RELATED DB: PDB
REMARK 900 RELATED ID: 7KBV RELATED DB: PDB
REMARK 900 RELATED ID: 7KBW RELATED DB: PDB
REMARK 900 RELATED ID: 30805 RELATED DB: BMRB
REMARK 900 SOLUTION STRUCTURE OF THE MAJOR MYC PROMOTER G-QUADRUPLEX IN
REMARK 900 COMPLEX WITH NSC85697, A QUINOLINE DERIVATIVE
DBREF 7KBX A 4 25 PDB 7KBX 7KBX 4 25
SEQRES 1 A 22 DT DG DA DG DG DG DT DG DG DG DT DA DG
SEQRES 2 A 22 DG DG DT DG DG DG DT DA DA
HET WAM A 101 44
HET WAM A 102 44
HETNAM WAM 2-[(~{E})-2-(3-METHOXY-4-OXIDANYL-PHENYL)ETHENYL]-1-
HETNAM 2 WAM METHYL-QUINOLINE-4-CARBOXAMIDE
FORMUL 2 WAM 2(C20 H19 N2 O3 1+)
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1