HEADER DNA 02-JUN-25 9VA0 TITLE SOLUTION NMR STRUCTURES OF HTERT DNA G-QUADRUPLEXES (G4S) IN COMPLEX TITLE 2 WITH SMALL MOLECULE CPT-11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*CP*TP*GP*GP*GP*AP*GP*GP*GP*CP*C)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEXES, TOPOISOMERASE I, CPT-11, IRINOTECAN, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.ZENG REVDAT 1 11-FEB-26 9VA0 0 JRNL AUTH Y.LI,D.JI,Y.JIA,Y.LIANG,E.WEI,C.GAO,Y.LI,C.ZENG,L.WANG, JRNL AUTH 2 C.WANG,Z.GUO,Y.ZHANG,M.-M.ZHOU,D.WU,L.ZENG JRNL TITL DUAL TARGETING OF TOPOISOMERASE I AND DNA G-QUADRUPLEXES JRNL TITL 2 ENHANCES SENESCENCE RESPONSE AND CHEMOSENSITIVITY IN JRNL TITL 3 COLORECTAL CANCER CELLS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9VA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300060104. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM POTASSIUM PHOSPHATE, 70 MM REMARK 210 POTASSIUM CHLORIDE, 100% D2O; 20 REMARK 210 MM POTASSIUM PHOSPHATE, 70 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, TOPSPIN, NMRPIPE REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 6 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 7 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 9 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 12 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 14 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 16 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 18 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 18 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 19 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 DT A 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES 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 11 0.08 SIDE CHAIN REMARK 500 2 DT A 11 0.08 SIDE CHAIN REMARK 500 3 DT A 11 0.07 SIDE CHAIN REMARK 500 4 DT A 11 0.07 SIDE CHAIN REMARK 500 5 DT A 11 0.09 SIDE CHAIN REMARK 500 6 DT A 11 0.08 SIDE CHAIN REMARK 500 7 DT A 11 0.08 SIDE CHAIN REMARK 500 8 DT A 11 0.07 SIDE CHAIN REMARK 500 9 DT A 11 0.07 SIDE CHAIN REMARK 500 10 DT A 11 0.08 SIDE CHAIN REMARK 500 11 DT A 11 0.08 SIDE CHAIN REMARK 500 12 DT A 11 0.07 SIDE CHAIN REMARK 500 13 DT A 11 0.08 SIDE CHAIN REMARK 500 14 DT A 11 0.06 SIDE CHAIN REMARK 500 15 DT A 11 0.08 SIDE CHAIN REMARK 500 16 DT A 11 0.09 SIDE CHAIN REMARK 500 17 DT A 11 0.07 SIDE CHAIN REMARK 500 18 DT A 11 0.08 SIDE CHAIN REMARK 500 19 DT A 11 0.08 SIDE CHAIN REMARK 500 20 DT A 11 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 501 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 DG A 5 O6 75.0 REMARK 620 3 DG A 8 O6 71.4 95.5 REMARK 620 4 DG A 9 O6 128.7 69.9 75.8 REMARK 620 5 DG A 14 O6 109.5 154.8 64.2 89.6 REMARK 620 6 DG A 15 O6 158.5 109.6 127.3 71.1 75.6 REMARK 620 7 DG A 18 O6 70.6 129.1 107.4 158.9 73.9 91.7 REMARK 620 8 DG A 19 O6 92.9 71.1 161.9 109.3 131.7 69.9 74.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 502 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 O6 REMARK 620 2 DG A 6 O6 75.2 REMARK 620 3 DG A 9 O6 70.2 97.0 REMARK 620 4 DG A 10 O6 127.7 71.3 75.4 REMARK 620 5 DG A 15 O6 109.7 163.7 71.2 94.4 REMARK 620 6 DG A 16 O6 163.5 105.9 125.3 66.6 74.1 REMARK 620 7 DG A 19 O6 71.5 125.6 110.0 159.7 70.1 95.7 REMARK 620 8 DG A 20 O6 91.9 63.7 157.1 107.1 130.2 74.4 75.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36761 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURES OF HTERT DNA G-QUADRUPLEXES (G4S) IN REMARK 900 COMPLEX WITH SMALL MOLECULE CPT-11 DBREF 9VA0 A 1 22 PDB 9VA0 9VA0 1 22 SEQRES 1 A 22 DA DA DT DG DG DG DA DG DG DG DT DC DT SEQRES 2 A 22 DG DG DG DA DG DG DG DC DC HET K A 501 1 HET K A 502 1 HET CP0 A 503 81 HETNAM K POTASSIUM ION HETNAM CP0 (4S)-4,11-DIETHYL-4-HYDROXY-3,14-DIOXO-3,4,12,14- HETNAM 2 CP0 TETRAHYDRO-1H-PYRANO[3',4':6,7]INDOLIZINO[1,2- HETNAM 3 CP0 B]QUINOLIN-9-YL 1,4'-BIPIPERIDINE-1'-CARBOXYLATE HETSYN CP0 IRINOTECAN; CPT-11 FORMUL 2 K 2(K 1+) FORMUL 4 CP0 C33 H38 N4 O6 LINK O6 DG A 4 K K A 501 1555 1555 2.80 LINK O6 DG A 5 K K A 501 1555 1555 2.81 LINK O6 DG A 5 K K A 502 1555 1555 2.80 LINK O6 DG A 6 K K A 502 1555 1555 2.80 LINK O6 DG A 8 K K A 501 1555 1555 2.79 LINK O6 DG A 9 K K A 501 1555 1555 2.81 LINK O6 DG A 9 K K A 502 1555 1555 2.80 LINK O6 DG A 10 K K A 502 1555 1555 2.80 LINK O6 DG A 14 K K A 501 1555 1555 2.80 LINK O6 DG A 15 K K A 501 1555 1555 2.80 LINK O6 DG A 15 K K A 502 1555 1555 2.81 LINK O6 DG A 16 K K A 502 1555 1555 2.80 LINK O6 DG A 18 K K A 501 1555 1555 2.79 LINK O6 DG A 19 K K A 501 1555 1555 2.81 LINK O6 DG A 19 K K A 502 1555 1555 2.79 LINK O6 DG A 20 K K A 502 1555 1555 2.80 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 111 711 CONECT 144 711 712 CONECT 177 712 CONECT 242 711 CONECT 275 711 712 CONECT 308 712 CONECT 435 711 CONECT 468 711 712 CONECT 501 712 CONECT 566 711 CONECT 599 711 712 CONECT 632 712 CONECT 711 111 144 242 275 CONECT 711 435 468 566 599 CONECT 712 144 177 275 308 CONECT 712 468 501 599 632 CONECT 713 721 732 CONECT 714 728 735 737 CONECT 715 727 CONECT 716 722 727 CONECT 717 735 CONECT 718 736 738 CONECT 719 738 CONECT 720 740 756 CONECT 721 713 725 730 CONECT 722 716 729 731 CONECT 723 728 734 757 CONECT 724 726 732 737 CONECT 725 721 726 729 CONECT 726 724 725 741 CONECT 727 715 716 744 CONECT 728 714 723 732 CONECT 729 722 725 758 CONECT 730 721 731 759 CONECT 731 722 730 760 CONECT 732 713 724 728 CONECT 733 734 735 736 CONECT 734 723 733 740 CONECT 735 714 717 733 CONECT 736 718 733 761 762 CONECT 737 714 724 763 764 CONECT 738 718 719 740 CONECT 739 740 743 765 766 CONECT 740 720 734 738 739 CONECT 741 726 742 767 768 CONECT 742 741 769 770 771 CONECT 743 739 772 773 774 CONECT 744 727 747 749 CONECT 745 748 750 752 CONECT 746 748 749 775 776 CONECT 747 744 755 777 778 CONECT 748 745 746 755 779 CONECT 749 744 746 780 781 CONECT 750 745 751 782 783 CONECT 751 750 754 784 785 CONECT 752 745 753 786 787 CONECT 753 752 754 788 789 CONECT 754 751 753 790 791 CONECT 755 747 748 792 793 CONECT 756 720 CONECT 757 723 CONECT 758 729 CONECT 759 730 CONECT 760 731 CONECT 761 736 CONECT 762 736 CONECT 763 737 CONECT 764 737 CONECT 765 739 CONECT 766 739 CONECT 767 741 CONECT 768 741 CONECT 769 742 CONECT 770 742 CONECT 771 742 CONECT 772 743 CONECT 773 743 CONECT 774 743 CONECT 775 746 CONECT 776 746 CONECT 777 747 CONECT 778 747 CONECT 779 748 CONECT 780 749 CONECT 781 749 CONECT 782 750 CONECT 783 750 CONECT 784 751 CONECT 785 751 CONECT 786 752 CONECT 787 752 CONECT 788 753 CONECT 789 753 CONECT 790 754 CONECT 791 754 CONECT 792 755 CONECT 793 755 MASTER 199 0 3 0 0 0 0 6 507 1 97 2 END