HEADER DNA 22-NOV-20 7DJV OBSLTE 03-APR-24 7DJV TITLE NMR SOLUTION STRUCTURE OF THE 2:1 COMPLEX OF A PLATINUM(II) COMPOUND TITLE 2 BOUND TO MYC1234 G-QUADRUPLEX REVEALS THE MECHANISM OF CONFORMATIONAL TITLE 3 SWITCH AND DYNAMIC BINDING OF G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYC1234 G-QUADRUPLEX 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 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, CONFORMATIONAL CONVERSION, BINDING DYNAMICS, DNA-LIGAND KEYWDS 2 COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.LIU,Z.W.MAO REVDAT 3 03-APR-24 7DJV 1 OBSLTE JRNL REVDAT 2 21-DEC-22 7DJV 1 JRNL REVDAT 1 12-JAN-22 7DJV 0 JRNL AUTH W.LIU,B.C.ZHU,L.Y.LIU,X.Y.XIA,Z.W.MAO JRNL TITL RETRACTED: G-QUADRUPLEX STRUCTURAL TRANSITION DRIVEN BY A JRNL TITL 2 PLATINUM COMPOUND JRNL REF NUCLEIC ACIDS RES. V. 50 7816 2022 JRNL REFN ESSN 1362-4962 JRNL DOI 10.1093/NAR/GKAC572 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, DISCOVERY STUDIO REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE. (X-PLOR REMARK 3 NIH), ACCELRYS (DISCOVERY STUDIO) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 PAPER RETRACTED REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019539. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15; 288.15; 278.15 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 20; 10; 10 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM MYC1234 G-QUADRUPLEX, 2.0 REMARK 210 MM PT-PHEN COMPOUND, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 10 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1.0 MM MYC1234 G-QUADRUPLEX, REMARK 210 2.0 MM PT-PHEN COMPOUND, 5 MM REMARK 210 POTASSIUM PHOSPHATE, 5 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 2D COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III 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 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: 36399 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 REVEALS THE MECHANISM OF REMARK 900 CONFORMATIONAL SWITCH AND DYNAMIC BINDING OF G-QUADRUPLEX DBREF 7DJV A 1 19 PDB 7DJV 7DJV 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