PDB Short entry for 2N6C HEADER DNA 18-AUG-15 2N6C TITLE SOLUTION STRUCTURE FOR QUERCETIN COMPLEXED WITH C-MYC G-QUADRUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP* COMPND 4 GP*G)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS C-MYC, QUERCETIN, FLAVONOIDS, G-QUADRUPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.KUMAR,A.TAWANI REVDAT 2 14-JUN-23 2N6C 1 REMARK REVDAT 1 14-SEP-16 2N6C 0 JRNL AUTH A.KUMAR,A.TAWANI JRNL TITL SOLUTION STRUCTURE FOR QUERCETIN COMPLEXED WITH C-MYC JRNL TITL 2 G-QUADRUPLEX DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, DISCOVERY STUDIO REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000104477. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.3 MM DNA (5' REMARK 210 -D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP* REMARK 210 AP*AP*GP*GP*P*)-3')-1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DT A 1 C4' DT A 1 C3' 0.116 REMARK 500 1 DT A 1 C5 DT A 1 C6 0.047 REMARK 500 1 DG A 2 N3 DG A 2 C4 -0.062 REMARK 500 1 DG A 2 C4 DG A 2 C5 0.056 REMARK 500 1 DG A 2 O3' DA A 3 P -0.086 REMARK 500 1 DA A 3 N3 DA A 3 C4 0.052 REMARK 500 1 DA A 3 N9 DA A 3 C4 0.045 REMARK 500 1 DG A 4 C5 DG A 4 N7 -0.052 REMARK 500 1 DG A 4 C8 DG A 4 N9 -0.059 REMARK 500 1 DG A 5 P DG A 5 O5' -0.090 REMARK 500 1 DG A 5 C3' DG A 5 C2' 0.089 REMARK 500 1 DG A 5 C4 DG A 5 C5 0.120 REMARK 500 1 DG A 5 C5 DG A 5 N7 -0.038 REMARK 500 1 DG A 5 N7 DG A 5 C8 0.052 REMARK 500 1 DG A 5 O3' DG A 6 P -0.076 REMARK 500 1 DG A 6 P DG A 6 O5' -0.125 REMARK 500 1 DT A 7 C6 DT A 7 N1 -0.086 REMARK 500 1 DT A 7 O3' DG A 8 P -0.080 REMARK 500 1 DG A 8 C2' DG A 8 C1' -0.086 REMARK 500 1 DG A 8 C5 DG A 8 N7 -0.085 REMARK 500 1 DG A 8 O3' DG A 9 P -0.074 REMARK 500 1 DG A 9 C5' DG A 9 C4' 0.074 REMARK 500 1 DG A 9 C3' DG A 9 C2' 0.113 REMARK 500 1 DG A 9 C2' DG A 9 C1' 0.091 REMARK 500 1 DG A 9 O3' DG A 9 C3' -0.044 REMARK 500 1 DG A 9 N9 DG A 9 C4 0.057 REMARK 500 1 DG A 9 O3' DT A 10 P -0.096 REMARK 500 1 DT A 10 P DT A 10 O5' -0.067 REMARK 500 1 DT A 10 C2 DT A 10 N3 0.080 REMARK 500 1 DT A 10 N3 DT A 10 C4 0.054 REMARK 500 1 DT A 10 C5 DT A 10 C6 0.078 REMARK 500 1 DT A 10 C5 DT A 10 C7 0.053 REMARK 500 1 DG A 11 P DG A 11 O5' -0.062 REMARK 500 1 DG A 11 C3' DG A 11 C2' -0.055 REMARK 500 1 DG A 11 N1 DG A 11 C2 -0.073 REMARK 500 1 DG A 11 N7 DG A 11 C8 0.060 REMARK 500 1 DA A 12 P DA A 12 O5' -0.119 REMARK 500 1 DA A 12 N7 DA A 12 C8 0.047 REMARK 500 1 DA A 12 C8 DA A 12 N9 -0.056 REMARK 500 1 DA A 12 N9 DA A 12 C4 0.044 REMARK 500 1 DG A 13 O4' DG A 13 C4' -0.063 REMARK 500 1 DG A 13 N1 DG A 13 C2 -0.068 REMARK 500 1 DG A 14 P DG A 14 O5' -0.087 REMARK 500 1 DG A 14 C5' DG A 14 C4' 0.074 REMARK 500 1 DG A 14 C4 DG A 14 C5 0.079 REMARK 500 1 DG A 14 N7 DG A 14 C8 0.046 REMARK 500 1 DG A 14 C8 DG A 14 N9 -0.077 REMARK 500 1 DG A 14 N9 DG A 14 C4 0.065 REMARK 500 1 DG A 15 P DG A 15 OP1 0.105 REMARK 500 1 DG A 15 P DG A 15 O5' -0.077 REMARK 500 REMARK 500 THIS ENTRY HAS 822 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 1 C2 - N3 - C4 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 2 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 2 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 2 N3 - C4 - C5 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 2 N3 - C4 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 2 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 3 C1' - O4' - C4' ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 3 N1 - C2 - N3 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DA A 3 C5 - N7 - C8 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 3 C6 - C5 - N7 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG A 4 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DG A 4 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 4 N9 - C4 - C5 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 5 O3' - P - O5' ANGL. DEV. = 13.7 DEGREES REMARK 500 1 DG A 5 OP1 - P - OP2 ANGL. DEV. = -14.7 DEGREES REMARK 500 1 DG A 5 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 5 C3' - C2' - C1' ANGL. DEV. = -10.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 5 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 5 N3 - C4 - C5 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 5 C4 - C5 - N7 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 5 N3 - C4 - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 6 OP1 - P - OP2 ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 6 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 7 OP1 - P - OP2 ANGL. DEV. = -12.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DT A 7 C4 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 8 O3' - P - O5' ANGL. DEV. = 16.0 DEGREES REMARK 500 1 DG A 8 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DG A 8 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 8 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 8 C5 - N7 - C8 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 8 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 9 C2 - N3 - C4 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DG A 9 N3 - C4 - C5 ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DG A 9 C4 - C5 - N7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 9 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1669 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 5 0.08 SIDE CHAIN REMARK 500 1 DG A 9 0.06 SIDE CHAIN REMARK 500 1 DA A 12 0.07 SIDE CHAIN REMARK 500 1 DG A 15 0.08 SIDE CHAIN REMARK 500 1 DG A 18 0.09 SIDE CHAIN REMARK 500 1 DG A 24 0.07 SIDE CHAIN REMARK 500 2 DG A 4 0.09 SIDE CHAIN REMARK 500 2 DA A 12 0.09 SIDE CHAIN REMARK 500 2 DG A 13 0.10 SIDE CHAIN REMARK 500 2 DG A 14 0.08 SIDE CHAIN REMARK 500 2 DG A 15 0.09 SIDE CHAIN REMARK 500 2 DG A 19 0.07 SIDE CHAIN REMARK 500 2 DG A 20 0.12 SIDE CHAIN REMARK 500 2 DG A 23 0.07 SIDE CHAIN REMARK 500 2 DG A 24 0.12 SIDE CHAIN REMARK 500 3 DG A 2 0.05 SIDE CHAIN REMARK 500 3 DA A 3 0.07 SIDE CHAIN REMARK 500 3 DG A 6 0.06 SIDE CHAIN REMARK 500 3 DA A 12 0.06 SIDE CHAIN REMARK 500 3 DG A 15 0.09 SIDE CHAIN REMARK 500 3 DG A 20 0.07 SIDE CHAIN REMARK 500 3 DG A 24 0.11 SIDE CHAIN REMARK 500 4 DG A 2 0.07 SIDE CHAIN REMARK 500 4 DA A 3 0.10 SIDE CHAIN REMARK 500 4 DG A 4 0.08 SIDE CHAIN REMARK 500 4 DG A 11 0.10 SIDE CHAIN REMARK 500 4 DA A 12 0.08 SIDE CHAIN REMARK 500 4 DG A 15 0.07 SIDE CHAIN REMARK 500 4 DG A 18 0.13 SIDE CHAIN REMARK 500 4 DG A 20 0.07 SIDE CHAIN REMARK 500 4 DA A 22 0.07 SIDE CHAIN REMARK 500 4 DG A 24 0.08 SIDE CHAIN REMARK 500 5 DG A 4 0.10 SIDE CHAIN REMARK 500 5 DG A 5 0.07 SIDE CHAIN REMARK 500 5 DG A 8 0.08 SIDE CHAIN REMARK 500 5 DT A 10 0.06 SIDE CHAIN REMARK 500 5 DA A 12 0.09 SIDE CHAIN REMARK 500 5 DG A 13 0.11 SIDE CHAIN REMARK 500 5 DG A 14 0.06 SIDE CHAIN REMARK 500 5 DG A 15 0.08 SIDE CHAIN REMARK 500 5 DG A 17 0.06 SIDE CHAIN REMARK 500 5 DG A 18 0.09 SIDE CHAIN REMARK 500 5 DG A 19 0.11 SIDE CHAIN REMARK 500 5 DG A 23 0.06 SIDE CHAIN REMARK 500 5 DG A 24 0.12 SIDE CHAIN REMARK 500 6 DG A 2 0.09 SIDE CHAIN REMARK 500 6 DG A 4 0.09 SIDE CHAIN REMARK 500 6 DG A 5 0.08 SIDE CHAIN REMARK 500 6 DG A 6 0.09 SIDE CHAIN REMARK 500 6 DG A 11 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 98 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QUE A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QUE A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25759 RELATED DB: BMRB DBREF 2N6C A 1 24 PDB 2N6C 2N6C 1 24 SEQRES 1 A 24 DT DG DA DG DG DG DT DG DG DT DG DA DG SEQRES 2 A 24 DG DG DT DG DG DG DG DA DA DG DG HET QUE A 101 32 HET QUE A 102 32 HETNAM QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE HETSYN QUE QUERCETIN FORMUL 2 QUE 2(C15 H10 O7) SITE 1 AC1 5 DG A 2 DG A 8 DA A 12 DG A 13 SITE 2 AC1 5 DG A 17 SITE 1 AC2 8 DG A 6 DT A 10 DG A 19 DG A 20 SITE 2 AC2 8 DA A 21 DA A 22 DG A 23 DG A 24 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