HEADER DNA 04-JUL-22 8ABD TITLE SOLUTION STRUCTURE OF PHEN-DC3 INTERCALATING INTO A QUADRUPLEX-DUPLEX TITLE 2 HYBRID COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (36-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, DUPLEX, QUADRUPLEX-DUPLEX JUNCTION, INTERCALATION, KEYWDS 2 PHEN-DC3, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.M.VIANNEY,K.WEISZ REVDAT 3 14-DEC-22 8ABD 1 JRNL REVDAT 2 07-DEC-22 8ABD 1 JRNL REVDAT 1 02-NOV-22 8ABD 0 JRNL AUTH Y.M.VIANNEY,K.WEISZ JRNL TITL HIGH-AFFINITY BINDING AT QUADRUPLEX-DUPLEX JUNCTIONS: RATHER JRNL TITL 2 THE RULE THAN THE EXCEPTION. JRNL REF NUCLEIC ACIDS RES. V. 50 11948 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36416262 JRNL DOI 10.1093/NAR/GKAC1088 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 18 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8ABD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292123133. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM NO DNA (37-MER), 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH 3.0.3, CCPNMR REMARK 210 ANALYSIS 2.4.2, TOPSPIN 4.0.7 REMARK 210 METHOD USED : SIMULATED 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL 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 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 5 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 19 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 21 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 21 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 21 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 24 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 24 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 24 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 25 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 25 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 25 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT A 26 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 26 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 27 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 27 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 28 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 29 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 30 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 31 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 31 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 31 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC A 32 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 34 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 34 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 34 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 35 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 36 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 473 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 DT A 23 0.06 SIDE CHAIN REMARK 500 1 DA A 25 0.06 SIDE CHAIN REMARK 500 2 DG A 4 0.10 SIDE CHAIN REMARK 500 2 DG A 18 0.05 SIDE CHAIN REMARK 500 2 DT A 26 0.09 SIDE CHAIN REMARK 500 3 DT A 2 0.07 SIDE CHAIN REMARK 500 3 DT A 33 0.07 SIDE CHAIN REMARK 500 4 DG A 4 0.05 SIDE CHAIN REMARK 500 4 DG A 7 0.06 SIDE CHAIN REMARK 500 4 DA A 25 0.07 SIDE CHAIN REMARK 500 4 DT A 29 0.08 SIDE CHAIN REMARK 500 5 DT A 2 0.06 SIDE CHAIN REMARK 500 5 DT A 23 0.06 SIDE CHAIN REMARK 500 5 DA A 25 0.06 SIDE CHAIN REMARK 500 5 DT A 33 0.07 SIDE CHAIN REMARK 500 6 DT A 2 0.07 SIDE CHAIN REMARK 500 6 DT A 23 0.07 SIDE CHAIN REMARK 500 6 DT A 33 0.06 SIDE CHAIN REMARK 500 6 DG A 36 0.07 SIDE CHAIN REMARK 500 7 DT A 2 0.07 SIDE CHAIN REMARK 500 7 DA A 25 0.06 SIDE CHAIN REMARK 500 7 DG A 36 0.05 SIDE CHAIN REMARK 500 8 DG A 4 0.06 SIDE CHAIN REMARK 500 8 DG A 7 0.05 SIDE CHAIN REMARK 500 8 DT A 15 0.09 SIDE CHAIN REMARK 500 8 DT A 23 0.06 SIDE CHAIN REMARK 500 8 DG A 36 0.07 SIDE CHAIN REMARK 500 9 DG A 4 0.06 SIDE CHAIN REMARK 500 9 DG A 7 0.05 SIDE CHAIN REMARK 500 9 DT A 26 0.08 SIDE CHAIN REMARK 500 9 DG A 36 0.07 SIDE CHAIN REMARK 500 10 DT A 33 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34740 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF PHEN-DC3 INTERCALATING INTO A QUADRUPLEX- REMARK 900 DUPLEX HYBRID REMARK 900 RELATED ID: 8ABN RELATED DB: PDB DBREF 8ABD A 1 36 PDB 8ABD 8ABD 1 36 SEQRES 1 A 36 THM DT DA DG DG DT DG DG DG DT DA DG DG SEQRES 2 A 36 DG DT DG DG DG DC DT DA DG DT DC DA DT SEQRES 3 A 36 DT DT DT DG DA DC DT DA DG DG HET THM A 1 30 HET PQ3 A 101 68 HETNAM THM THYMIDINE HETNAM PQ3 N2,N9-BIS(1-METHYLQUINOLIN-3-YL)-1,10-PHENANTHROLINE-2, HETNAM 2 PQ3 9-DICARBOXAMIDE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE HETSYN PQ3 PHEN-DC3 FORMUL 1 THM C10 H14 N2 O5 FORMUL 2 PQ3 C34 H26 N6 O2 LINK O3' THM A 1 P DT A 2 1555 1555 1.61 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 HETATM 1 O5' THM A 1 19.283 47.288 23.607 1.00 0.00 O HETATM 2 C5' THM A 1 19.488 47.745 24.944 1.00 0.00 C HETATM 3 C4' THM A 1 20.945 47.596 25.417 1.00 0.00 C HETATM 4 O4' THM A 1 21.383 46.249 25.313 1.00 0.00 O HETATM 5 C3' THM A 1 21.948 48.404 24.590 1.00 0.00 C HETATM 6 O3' THM A 1 21.999 49.762 25.007 1.00 0.00 O HETATM 7 C2' THM A 1 23.251 47.654 24.873 1.00 0.00 C HETATM 8 C1' THM A 1 22.801 46.252 25.319 1.00 0.00 C HETATM 9 N1 THM A 1 23.307 45.141 24.458 1.00 0.00 N HETATM 10 C2 THM A 1 24.132 44.176 25.051 1.00 0.00 C HETATM 11 O2 THM A 1 24.364 44.120 26.256 1.00 0.00 O HETATM 12 N3 THM A 1 24.721 43.253 24.220 1.00 0.00 N HETATM 13 C4 THM A 1 24.534 43.167 22.858 1.00 0.00 C HETATM 14 O4 THM A 1 25.153 42.310 22.231 1.00 0.00 O HETATM 15 C5 THM A 1 23.605 44.152 22.303 1.00 0.00 C HETATM 16 C5M THM A 1 23.291 44.150 20.816 1.00 0.00 C HETATM 17 C6 THM A 1 23.031 45.093 23.103 1.00 0.00 C HETATM 18 HO5' THM A 1 19.505 46.335 23.559 1.00 0.00 H HETATM 19 H5'1 THM A 1 18.843 47.185 25.624 1.00 0.00 H HETATM 20 H5'2 THM A 1 19.210 48.799 25.010 1.00 0.00 H HETATM 21 H4' THM A 1 21.014 47.918 26.459 1.00 0.00 H HETATM 22 H3' THM A 1 21.684 48.327 23.534 1.00 0.00 H HETATM 23 H2'1 THM A 1 23.889 47.634 23.991 1.00 0.00 H HETATM 24 H2'2 THM A 1 23.791 48.131 25.693 1.00 0.00 H HETATM 25 H1' THM A 1 23.146 46.107 26.348 1.00 0.00 H HETATM 26 HN3 THM A 1 25.381 42.622 24.642 1.00 0.00 H HETATM 27 HM51 THM A 1 24.218 44.258 20.252 1.00 0.00 H HETATM 28 HM52 THM A 1 22.615 44.964 20.552 1.00 0.00 H HETATM 29 HM53 THM A 1 22.833 43.198 20.544 1.00 0.00 H HETATM 30 H6 THM A 1 22.338 45.805 22.674 1.00 0.00 H