HEADER DNA 24-SEP-24 9GVI TITLE QUADRUPLEX-DUPLEX HYBRIDS (QDH) COMPLEX WITH PHENDC3 FROM PIM1 TITLE 2 ONCOGENE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (27-MER) COMPLEX WITH LIGAND (PHENDC3); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: QGCGGGAGGGCGCGCCAGCGGGGTCGGG SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX DNA, PIM1 ONCOGENE, THE TRIPLE-NEGATIVE BREAST CANCER, KEYWDS 2 DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.GHOSH,M.Z.LENARCIC,L.TRANTIREK,J.HARNOS REVDAT 2 01-OCT-25 9GVI 1 JRNL REVDAT 1 27-AUG-25 9GVI 0 JRNL AUTH A.GHOSH,J.HARNOS,P.STADLBAUER,J.SPONER,M.LENARCIC ZIVKOVIC, JRNL AUTH 2 L.TRANTIREK JRNL TITL STRUCTURAL BASIS OF BIS-QUINOLINIUM LIGANDS BINDING TO JRNL TITL 2 QUADRUPLEX-DUPLEX HYBRIDS FROM PIM1 ONCOGENE. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40966494 JRNL DOI 10.1093/NAR/GKAF894 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 22 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 9GVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292138734. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.2 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM NA SO7-PHENDC3, 200 UM [U REMARK 210 -13C; U-15N]-GUANINE SO7-PHENDC3, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC AROMATIC; 2D 1H REMARK 210 -15N HSQC; 2D NOESY; 2D 1H-1H REMARK 210 TOCSY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 950 MHZ; 850 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY 1.414, AMBER 22 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 DG A 1 C5 DG A 1 N7 -0.047 REMARK 500 1 DG A 1 O3' DC A 2 P 0.115 REMARK 500 1 DC A 2 P DC A 2 O5' 0.128 REMARK 500 1 DC A 2 C2 DC A 2 N3 0.058 REMARK 500 1 DC A 2 N3 DC A 2 C4 -0.050 REMARK 500 1 DC A 2 O3' DG A 3 P 0.125 REMARK 500 1 DG A 3 P DG A 3 O5' 0.138 REMARK 500 1 DG A 3 C5 DG A 3 N7 -0.048 REMARK 500 1 DG A 3 O3' DG A 4 P 0.128 REMARK 500 1 DG A 4 P DG A 4 O5' 0.134 REMARK 500 1 DG A 4 C5 DG A 4 N7 -0.049 REMARK 500 1 DG A 4 O3' DG A 5 P 0.116 REMARK 500 1 DG A 5 P DG A 5 O5' 0.130 REMARK 500 1 DG A 5 C5 DG A 5 N7 -0.046 REMARK 500 1 DG A 5 O3' DA A 6 P 0.125 REMARK 500 1 DA A 6 P DA A 6 O5' 0.133 REMARK 500 1 DA A 6 C5 DA A 6 N7 -0.046 REMARK 500 1 DA A 6 C6 DA A 6 N6 0.058 REMARK 500 1 DA A 6 O3' DG A 7 P 0.125 REMARK 500 1 DG A 7 P DG A 7 O5' 0.136 REMARK 500 1 DG A 7 C5 DG A 7 N7 -0.047 REMARK 500 1 DG A 7 O3' DG A 8 P 0.136 REMARK 500 1 DG A 8 P DG A 8 O5' 0.130 REMARK 500 1 DG A 8 C5 DG A 8 N7 -0.049 REMARK 500 1 DG A 8 O3' DG A 9 P 0.120 REMARK 500 1 DG A 9 P DG A 9 O5' 0.132 REMARK 500 1 DG A 9 C5 DG A 9 N7 -0.049 REMARK 500 1 DG A 9 O3' DC A 10 P 0.131 REMARK 500 1 DC A 10 P DC A 10 O5' 0.134 REMARK 500 1 DC A 10 C2 DC A 10 N3 0.057 REMARK 500 1 DC A 10 N3 DC A 10 C4 -0.051 REMARK 500 1 DC A 10 O3' DG A 11 P 0.114 REMARK 500 1 DG A 11 P DG A 11 O5' 0.130 REMARK 500 1 DG A 11 C5 DG A 11 N7 -0.046 REMARK 500 1 DG A 11 O3' DC A 12 P 0.129 REMARK 500 1 DC A 12 P DC A 12 O5' 0.132 REMARK 500 1 DC A 12 C2 DC A 12 N3 0.056 REMARK 500 1 DC A 12 N3 DC A 12 C4 -0.051 REMARK 500 1 DC A 12 O3' DG A 13 P 0.124 REMARK 500 1 DG A 13 P DG A 13 O5' 0.131 REMARK 500 1 DG A 13 C5 DG A 13 N7 -0.046 REMARK 500 1 DG A 13 O3' DC A 14 P 0.124 REMARK 500 1 DC A 14 P DC A 14 O5' 0.133 REMARK 500 1 DC A 14 C2 DC A 14 N3 0.061 REMARK 500 1 DC A 14 N3 DC A 14 C4 -0.049 REMARK 500 1 DC A 14 O3' DC A 15 P 0.123 REMARK 500 1 DC A 15 P DC A 15 O5' 0.138 REMARK 500 1 DC A 15 C2 DC A 15 N3 0.058 REMARK 500 1 DC A 15 N3 DC A 15 C4 -0.050 REMARK 500 1 DC A 15 O3' DA A 16 P 0.124 REMARK 500 REMARK 500 THIS ENTRY HAS 870 BOND DEVIATIONS. 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC A 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 18 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 19 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 24 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 25 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 26 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 27 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 16 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 18 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG A 19 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 22 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DT A 23 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 24 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 25 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 26 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 27 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 242 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 DG A 9 0.06 SIDE CHAIN REMARK 500 1 DC A 12 0.11 SIDE CHAIN REMARK 500 1 DG A 17 0.06 SIDE CHAIN REMARK 500 2 DC A 12 0.09 SIDE CHAIN REMARK 500 2 DG A 22 0.09 SIDE CHAIN REMARK 500 2 DC A 24 0.10 SIDE CHAIN REMARK 500 3 DC A 12 0.11 SIDE CHAIN REMARK 500 3 DG A 22 0.06 SIDE CHAIN REMARK 500 4 DC A 12 0.11 SIDE CHAIN REMARK 500 4 DG A 17 0.06 SIDE CHAIN REMARK 500 5 DC A 12 0.11 SIDE CHAIN REMARK 500 5 DG A 22 0.07 SIDE CHAIN REMARK 500 6 DG A 9 0.08 SIDE CHAIN REMARK 500 6 DC A 12 0.08 SIDE CHAIN REMARK 500 6 DG A 22 0.06 SIDE CHAIN REMARK 500 6 DC A 24 0.09 SIDE CHAIN REMARK 500 7 DC A 12 0.12 SIDE CHAIN REMARK 500 7 DG A 22 0.08 SIDE CHAIN REMARK 500 7 DC A 24 0.10 SIDE CHAIN REMARK 500 8 DC A 12 0.12 SIDE CHAIN REMARK 500 9 DC A 12 0.12 SIDE CHAIN REMARK 500 9 DG A 22 0.07 SIDE CHAIN REMARK 500 9 DC A 24 0.09 SIDE CHAIN REMARK 500 10 DC A 12 0.12 SIDE CHAIN REMARK 500 10 DC A 15 0.08 SIDE CHAIN REMARK 500 10 DG A 17 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34960 RELATED DB: BMRB REMARK 900 QUADRUPLEX-DUPLEX HYBRIDS (QDH) COMPLEX WITH PHENDC3 FROM PIM1 REMARK 900 ONCOGENE. DBREF 9GVI A 1 27 PDB 9GVI 9GVI 1 27 SEQRES 1 A 27 DG DC DG DG DG DA DG DG DG DC DG DC DG SEQRES 2 A 27 DC DC DA DG DC DG DG DG DG DT DC DG DG SEQRES 3 A 27 DG HET PQ3 A 101 68 HETNAM PQ3 N2,N9-BIS(1-METHYLQUINOLIN-3-YL)-1,10-PHENANTHROLINE-2, HETNAM 2 PQ3 9-DICARBOXAMIDE HETSYN PQ3 PHEN-DC3 FORMUL 2 PQ3 C34 H26 N6 O2 2+ 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 868 869 870 910 CONECT 869 868 879 902 CONECT 870 868 871 911 CONECT 871 870 872 875 CONECT 872 871 873 902 CONECT 873 872 874 906 CONECT 874 873 880 881 CONECT 875 871 880 912 CONECT 876 907 913 914 915 CONECT 877 884 895 916 CONECT 878 882 883 906 CONECT 879 869 903 909 CONECT 880 874 875 917 CONECT 881 874 882 918 CONECT 882 878 881 919 CONECT 883 878 905 908 CONECT 884 877 891 920 CONECT 885 886 889 905 CONECT 886 885 887 921 CONECT 887 886 888 890 CONECT 888 887 892 904 CONECT 889 885 904 922 CONECT 890 887 893 923 CONECT 891 884 900 924 CONECT 892 888 894 925 CONECT 893 890 894 926 CONECT 894 892 893 927 CONECT 895 877 899 928 CONECT 896 897 898 903 CONECT 897 896 907 929 CONECT 898 896 899 930 CONECT 899 895 898 900 CONECT 900 891 899 907 CONECT 901 904 931 932 933 CONECT 902 869 872 CONECT 903 879 896 934 CONECT 904 888 889 901 CONECT 905 883 885 935 CONECT 906 873 878 CONECT 907 876 897 900 CONECT 908 883 CONECT 909 879 CONECT 910 868 CONECT 911 870 CONECT 912 875 CONECT 913 876 CONECT 914 876 CONECT 915 876 CONECT 916 877 CONECT 917 880 CONECT 918 881 CONECT 919 882 CONECT 920 884 CONECT 921 886 CONECT 922 889 CONECT 923 890 CONECT 924 891 CONECT 925 892 CONECT 926 893 CONECT 927 894 CONECT 928 895 CONECT 929 897 CONECT 930 898 CONECT 931 901 CONECT 932 901 CONECT 933 901 CONECT 934 903 CONECT 935 905 MASTER 255 0 1 0 0 0 0 6 608 1 68 3 END