HEADER DNA 26-MAR-24 8YU3 TITLE NMR SOLUTION STRUCTURE OF THE 2:1 COMPLEX OF A PLATINUM(II) COMPOUND TITLE 2 BOUND TO MYC1234 G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS G-QUADRUPLEX, DNA-LIGAND COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.LIU,Z.W.MAO REVDAT 1 09-APR-25 8YU3 0 JRNL AUTH W.LIU,B.C.ZHU,L.Y.LIU,X.Y.XIA,J.JANG,J.DICKERHOFF,D.YANG, JRNL AUTH 2 Z.W.MAO JRNL TITL SOLUTION STRUCTURES AND EFFECTS OF A PLATINUM COMPOUND JRNL TITL 2 SUCCESSIVELY BOUND MYC G-QUADRUPLEX. JRNL REF NUCLEIC ACIDS RES. V. 52 9397 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39077944 JRNL DOI 10.1093/NAR/GKAE649 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVERY STUDIO, X-PLOR NIH REMARK 3 AUTHORS : ACCELRYS SOFTWARE INC. (DISCOVERY STUDIO), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8YU3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300046394. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1.0 MM NA-K DNA (5' REMARK 210 -D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), REMARK 210 2.0 MM NA-K PT-PHEN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 2D COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING 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: 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 C5 DT A 1 C7 0.052 REMARK 500 1 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 1 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 2 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 2 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 2 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 3 DT A 1 C5 DT A 1 C7 0.052 REMARK 500 3 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 3 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 4 DT A 1 C5 DT A 1 C7 0.052 REMARK 500 4 DT A 10 C5 DT A 10 C7 0.053 REMARK 500 4 DT A 19 C5 DT A 19 C7 0.051 REMARK 500 5 DT A 1 C5 DT A 1 C7 0.052 REMARK 500 5 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 5 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 6 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 6 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 6 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 7 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 7 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 7 DT A 19 C5 DT A 19 C7 0.051 REMARK 500 8 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 8 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 8 DT A 19 C5 DT A 19 C7 0.051 REMARK 500 9 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 9 DT A 10 C5 DT A 10 C7 0.053 REMARK 500 9 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 10 DT A 1 C5 DT A 1 C7 0.052 REMARK 500 10 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 10 DT A 19 C5 DT A 19 C7 0.052 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 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 11 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 11 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 13 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 14 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 14 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 15 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 15 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 17 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 509 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36653 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE 2:1 COMPLEX OF A PLATINUM(II) REMARK 900 COMPOUND BOUND TO MYC1234 G-QUADRUPLEX DBREF 8YU3 A 1 19 PDB 8YU3 8YU3 1 19 SEQRES 1 A 19 DT DA DG DG DG DA DG DG DG DT DA DG DG SEQRES 2 A 19 DG DA DG DG DG DT HET H9C A 101 45 HET H9C A 102 45 HETNAM H9C BIS(1,10-PHENANTHROLINE)PLATINUM(II) FORMUL 2 H9C 2(C24 H16 N4 PT) 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 621 622 634 649 CONECT 622 621 623 650 CONECT 623 622 624 651 CONECT 624 623 625 652 CONECT 625 624 626 634 CONECT 626 625 627 653 CONECT 627 626 628 654 CONECT 628 627 629 633 CONECT 629 628 630 655 CONECT 630 629 631 656 CONECT 631 630 632 657 CONECT 632 631 633 649 CONECT 633 628 632 634 CONECT 634 621 625 633 CONECT 635 636 648 649 CONECT 636 635 637 658 CONECT 637 636 638 659 CONECT 638 637 639 660 CONECT 639 638 640 648 CONECT 640 639 641 661 CONECT 641 640 642 662 CONECT 642 641 643 647 CONECT 643 642 644 663 CONECT 644 643 645 664 CONECT 645 644 646 665 CONECT 646 645 647 649 CONECT 647 642 646 648 CONECT 648 635 639 647 CONECT 649 621 632 635 646 CONECT 650 622 CONECT 651 623 CONECT 652 624 CONECT 653 626 CONECT 654 627 CONECT 655 629 CONECT 656 630 CONECT 657 631 CONECT 658 636 CONECT 659 637 CONECT 660 638 CONECT 661 640 CONECT 662 641 CONECT 663 643 CONECT 664 644 CONECT 665 645 CONECT 666 667 679 694 CONECT 667 666 668 695 CONECT 668 667 669 696 CONECT 669 668 670 697 CONECT 670 669 671 679 CONECT 671 670 672 698 CONECT 672 671 673 699 CONECT 673 672 674 678 CONECT 674 673 675 700 CONECT 675 674 676 701 CONECT 676 675 677 702 CONECT 677 676 678 694 CONECT 678 673 677 679 CONECT 679 666 670 678 CONECT 680 681 693 694 CONECT 681 680 682 703 CONECT 682 681 683 704 CONECT 683 682 684 705 CONECT 684 683 685 693 CONECT 685 684 686 706 CONECT 686 685 687 707 CONECT 687 686 688 692 CONECT 688 687 689 708 CONECT 689 688 690 709 CONECT 690 689 691 710 CONECT 691 690 692 694 CONECT 692 687 691 693 CONECT 693 680 684 692 CONECT 694 666 677 680 691 CONECT 695 667 CONECT 696 668 CONECT 697 669 CONECT 698 671 CONECT 699 672 CONECT 700 674 CONECT 701 675 CONECT 702 676 CONECT 703 681 CONECT 704 682 CONECT 705 683 CONECT 706 685 CONECT 707 686 CONECT 708 688 CONECT 709 689 CONECT 710 690 MASTER 194 0 2 0 0 0 0 6 463 1 90 2 END