HEADER DNA 24-SEP-24 9DQE TITLE NMR SOLUTION STRUCTURE OF THE 2:1 COPTISINE- BLM-G4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T*(LIG COMPND 4 )*(LIG))-3'); COMPND 5 CHAIN: X; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS BLM PROMOTER, G-QUADRUPLEX, DNA, COPTISINE, COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.B.WANG REVDAT 1 08-APR-26 9DQE 0 JRNL AUTH Y.Y.WANG,Y.T.BIAN,X.Y.CHEN,J.Z.LI,Y.S.LIU,L.Y.KONG,K.B.WANG JRNL TITL BLM G-QUADRUPLEX STABILIZERS SYNERGIZE WITH PARP INHIBITOR JRNL TITL 2 TO KILL BRCA WILD-TYPE COLON CANCER CELLS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 9DQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000288626. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 308 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 50; 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.62 MM NONE BLM_PU21T_COP, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, X-PLOR NIH, NMRFAM REMARK 210 -SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 APPLY THE FOLLOWING TO CHAINS: X 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 X 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT X 1 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG X 2 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 3 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 3 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 7 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG X 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC X 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG X 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA X 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 15 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG X 18 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA X 19 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA X 19 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 19 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA X 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA X 20 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 20 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 20 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT X 21 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT X 21 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT X 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT X 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG X 2 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 3 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA X 3 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG X 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG X 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 7 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC X 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DG X 12 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG X 13 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG X 14 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA X 15 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA X 15 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA X 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 15 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DG X 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 297 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 2 DG X 2 0.06 SIDE CHAIN REMARK 500 2 DG X 16 0.07 SIDE CHAIN REMARK 500 3 DG X 2 0.06 SIDE CHAIN REMARK 500 3 DG X 16 0.06 SIDE CHAIN REMARK 500 4 DG X 2 0.05 SIDE CHAIN REMARK 500 4 DG X 16 0.05 SIDE CHAIN REMARK 500 5 DG X 8 0.06 SIDE CHAIN REMARK 500 6 DG X 2 0.05 SIDE CHAIN REMARK 500 7 DG X 2 0.05 SIDE CHAIN REMARK 500 7 DG X 16 0.07 SIDE CHAIN REMARK 500 8 DG X 16 0.06 SIDE CHAIN REMARK 500 9 DG X 2 0.06 SIDE CHAIN REMARK 500 9 DG X 16 0.06 SIDE CHAIN REMARK 500 10 DG X 2 0.05 SIDE CHAIN REMARK 500 10 DG X 16 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31206 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE 2:1 COPTISINE- BLM-G4 COMPLEX DBREF 9DQE X 1 21 PDB 9DQE 9DQE 1 21 SEQRES 1 X 21 DT DG DA DG DG DG DA DG DG DG DC DG DG SEQRES 2 X 21 DG DA DG DG DG DA DA DT HET KPT X 101 38 HET KPT X 102 38 HETNAM KPT 6,7-DIHYDRO[1,3]DIOXOLO[4,5-G][1,3]DIOXOLO[7, HETNAM 2 KPT 8]ISOQUINO[3,2-A]ISOQUINOLIN-5-IUM HETSYN KPT COPTISINE FORMUL 2 KPT 2(C19 H14 N O4 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 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 CONECT 684 685 686 708 709 CONECT 685 684 690 CONECT 686 684 687 CONECT 687 686 688 690 CONECT 688 687 689 693 CONECT 689 688 696 710 CONECT 690 685 687 691 CONECT 691 690 692 711 CONECT 692 691 693 712 CONECT 693 688 692 694 CONECT 694 693 695 713 CONECT 695 694 696 699 CONECT 696 689 695 697 CONECT 697 696 698 714 715 CONECT 698 697 700 716 717 CONECT 699 695 700 702 CONECT 700 698 699 701 CONECT 701 700 704 718 CONECT 702 699 703 719 CONECT 703 702 704 706 CONECT 704 701 703 705 CONECT 705 704 707 CONECT 706 703 707 CONECT 707 705 706 720 721 CONECT 708 684 CONECT 709 684 CONECT 710 689 CONECT 711 691 CONECT 712 692 CONECT 713 694 CONECT 714 697 CONECT 715 697 CONECT 716 698 CONECT 717 698 CONECT 718 701 CONECT 719 702 CONECT 720 707 CONECT 721 707 CONECT 722 723 724 746 747 CONECT 723 722 728 CONECT 724 722 725 CONECT 725 724 726 728 CONECT 726 725 727 731 CONECT 727 726 734 748 CONECT 728 723 725 729 CONECT 729 728 730 749 CONECT 730 729 731 750 CONECT 731 726 730 732 CONECT 732 731 733 751 CONECT 733 732 734 737 CONECT 734 727 733 735 CONECT 735 734 736 752 753 CONECT 736 735 738 754 755 CONECT 737 733 738 740 CONECT 738 736 737 739 CONECT 739 738 742 756 CONECT 740 737 741 757 CONECT 741 740 742 744 CONECT 742 739 741 743 CONECT 743 742 745 CONECT 744 741 745 CONECT 745 743 744 758 759 CONECT 746 722 CONECT 747 722 CONECT 748 727 CONECT 749 729 CONECT 750 730 CONECT 751 732 CONECT 752 735 CONECT 753 735 CONECT 754 736 CONECT 755 736 CONECT 756 739 CONECT 757 740 CONECT 758 745 CONECT 759 745 MASTER 174 0 2 0 0 0 0 6 495 1 76 2 END