HEADER DNA 25-SEP-24 9GVV TITLE QUADRUPLEX-DUPLEX HYBRID (QDH) COMPLEX WITH 360A FROM PIM1 ONCOGENE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: QUADRUPLEX-DUPLEX HYBRID 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,J.HARNOS,L.TRANTIREK REVDAT 2 01-OCT-25 9GVV 1 JRNL REVDAT 1 27-AUG-25 9GVV 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 9GVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292142019. 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 SO7-360A, 90% H2O/10% REMARK 210 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 -0.048 REMARK 500 1 DG A 1 O3' DC A 2 P 0.114 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 -0.051 REMARK 500 1 DC A 2 O3' DG A 3 P 0.125 REMARK 500 1 DG A 3 P DG A 3 O5' 0.139 REMARK 500 1 DG A 3 C5 DG A 3 N7 -0.048 REMARK 500 1 DG A 3 O3' DG A 4 P 0.130 REMARK 500 1 DG A 4 P DG A 4 O5' 0.135 REMARK 500 1 DG A 4 C5 DG A 4 N7 -0.048 REMARK 500 1 DG A 4 O3' DG A 5 P 0.128 REMARK 500 1 DG A 5 P DG A 5 O5' 0.139 REMARK 500 1 DG A 5 C5 DG A 5 N7 -0.047 REMARK 500 1 DG A 5 O3' DA A 6 P 0.129 REMARK 500 1 DA A 6 P DA A 6 O5' 0.136 REMARK 500 1 DA A 6 C5 DA A 6 N7 -0.045 REMARK 500 1 DA A 6 C6 DA A 6 N6 0.057 REMARK 500 1 DA A 6 O3' DG A 7 P 0.126 REMARK 500 1 DG A 7 P DG A 7 O5' 0.130 REMARK 500 1 DG A 7 C5 DG A 7 N7 -0.048 REMARK 500 1 DG A 7 O3' DG A 8 P 0.123 REMARK 500 1 DG A 8 P DG A 8 O5' 0.132 REMARK 500 1 DG A 8 C5 DG A 8 N7 -0.049 REMARK 500 1 DG A 8 O3' DG A 9 P 0.119 REMARK 500 1 DG A 9 P DG A 9 O5' 0.129 REMARK 500 1 DG A 9 C5 DG A 9 N7 -0.047 REMARK 500 1 DG A 9 O3' DC A 10 P 0.125 REMARK 500 1 DC A 10 P DC A 10 O5' 0.135 REMARK 500 1 DC A 10 C2 DC A 10 N3 0.059 REMARK 500 1 DC A 10 N3 DC A 10 C4 -0.050 REMARK 500 1 DC A 10 O3' DG A 11 P 0.127 REMARK 500 1 DG A 11 P DG A 11 O5' 0.133 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 -0.050 REMARK 500 1 DC A 12 O3' DG A 13 P 0.121 REMARK 500 1 DG A 13 P DG A 13 O5' 0.138 REMARK 500 1 DG A 13 C5 DG A 13 N7 -0.047 REMARK 500 1 DG A 13 O3' DC A 14 P 0.121 REMARK 500 1 DC A 14 P DC A 14 O5' 0.139 REMARK 500 1 DC A 14 C2 DC A 14 N3 0.059 REMARK 500 1 DC A 14 N3 DC A 14 C4 -0.050 REMARK 500 1 DC A 14 O3' DC A 15 P 0.125 REMARK 500 1 DC A 15 P DC A 15 O5' 0.127 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 0.129 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. = 3.5 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 24 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 25 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 26 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 27 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 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. = 4.0 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 15 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 16 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 19 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 22 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DC A 24 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG A 25 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 26 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG A 27 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 226 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 DC A 10 0.06 SIDE CHAIN REMARK 500 1 DC A 12 0.08 SIDE CHAIN REMARK 500 2 DC A 10 0.09 SIDE CHAIN REMARK 500 2 DG A 22 0.06 SIDE CHAIN REMARK 500 3 DC A 10 0.11 SIDE CHAIN REMARK 500 3 DC A 12 0.10 SIDE CHAIN REMARK 500 3 DC A 15 0.07 SIDE CHAIN REMARK 500 4 DC A 10 0.09 SIDE CHAIN REMARK 500 4 DC A 12 0.09 SIDE CHAIN REMARK 500 4 DG A 22 0.06 SIDE CHAIN REMARK 500 5 DC A 10 0.09 SIDE CHAIN REMARK 500 5 DC A 12 0.11 SIDE CHAIN REMARK 500 5 DC A 15 0.08 SIDE CHAIN REMARK 500 5 DG A 22 0.06 SIDE CHAIN REMARK 500 6 DG A 9 0.06 SIDE CHAIN REMARK 500 6 DC A 10 0.08 SIDE CHAIN REMARK 500 6 DC A 12 0.09 SIDE CHAIN REMARK 500 6 DC A 24 0.07 SIDE CHAIN REMARK 500 7 DC A 10 0.07 SIDE CHAIN REMARK 500 7 DC A 12 0.09 SIDE CHAIN REMARK 500 7 DG A 20 0.06 SIDE CHAIN REMARK 500 8 DC A 10 0.10 SIDE CHAIN REMARK 500 8 DC A 12 0.07 SIDE CHAIN REMARK 500 9 DG A 5 0.06 SIDE CHAIN REMARK 500 9 DC A 10 0.09 SIDE CHAIN REMARK 500 9 DC A 12 0.08 SIDE CHAIN REMARK 500 9 DG A 22 0.05 SIDE CHAIN REMARK 500 10 DC A 10 0.10 SIDE CHAIN REMARK 500 10 DC A 12 0.08 SIDE CHAIN REMARK 500 10 DC A 15 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34961 RELATED DB: BMRB REMARK 900 QUADRUPLEX-DUPLEX HYBRID (QDH) COMPLEX WITH 360A FROM PIM1 ONCOGENE. DBREF 9GVV A 1 27 PDB 9GVV 9GVV 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 LWQ A 101 57 HETNAM LWQ ~{N}2,~{N}6-BIS(1-METHYLQUINOLIN-1-IUM-3-YL)PYRIDINE-2, HETNAM 2 LWQ 6-DICARBOXAMIDE FORMUL 2 LWQ C27 H23 N5 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 868 885 886 CONECT 869 872 874 902 CONECT 870 871 886 903 CONECT 871 870 884 904 CONECT 872 869 885 887 CONECT 873 886 888 889 CONECT 874 869 875 876 CONECT 875 874 891 905 CONECT 876 874 893 906 CONECT 877 894 895 907 CONECT 878 893 895 908 CONECT 879 897 898 900 CONECT 880 890 898 909 CONECT 881 897 899 910 CONECT 882 899 900 911 CONECT 883 891 912 913 914 CONECT 884 871 885 915 CONECT 885 868 872 884 CONECT 886 868 870 873 CONECT 887 872 CONECT 888 873 890 916 CONECT 889 873 CONECT 890 880 888 896 CONECT 891 875 883 892 CONECT 892 891 893 894 CONECT 893 876 878 892 CONECT 894 877 892 917 CONECT 895 877 878 918 CONECT 896 890 897 919 CONECT 897 879 881 896 CONECT 898 879 880 901 CONECT 899 881 882 920 CONECT 900 879 882 921 CONECT 901 898 922 923 924 CONECT 902 869 CONECT 903 870 CONECT 904 871 CONECT 905 875 CONECT 906 876 CONECT 907 877 CONECT 908 878 CONECT 909 880 CONECT 910 881 CONECT 911 882 CONECT 912 883 CONECT 913 883 CONECT 914 883 CONECT 915 884 CONECT 916 888 CONECT 917 894 CONECT 918 895 CONECT 919 896 CONECT 920 899 CONECT 921 900 CONECT 922 901 CONECT 923 901 CONECT 924 901 MASTER 257 0 1 0 0 0 0 6 600 1 57 3 END