HEADER DNA 06-SEP-21 7PNE TITLE PARALLEL Q-D HYBRID WITH 3' DUPLEX STEM-LOOP AS A LATERAL SNAPBACK TITLE 2 LOOP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TTAMYCDUP-3SBL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS G-QUADRUPLEX, DUPLEX, QUADRUPLEX-DUPLEX JUNCTION, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.M.VIANNEY,K.WEISZ REVDAT 5 19-JUN-24 7PNE 1 REMARK REVDAT 4 16-FEB-22 7PNE 1 JRNL REVDAT 3 09-FEB-22 7PNE 1 JRNL REVDAT 2 19-JAN-22 7PNE 1 JRNL REVDAT 1 29-DEC-21 7PNE 0 JRNL AUTH Y.M.VIANNEY,K.WEISZ JRNL TITL INDOLOQUINOLINE LIGANDS FAVOR INTERCALATION AT JRNL TITL 2 QUADRUPLEX-DUPLEX INTERFACES. JRNL REF CHEMISTRY V. 28 03718 2022 JRNL REFN ISSN 0947-6539 JRNL PMID 34905232 JRNL DOI 10.1002/CHEM.202103718 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 16 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 7PNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292118011. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM 0 DNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC AROMATIC; 2D 1H REMARK 210 -1H NOESY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4.2, TOPSPIN REMARK 210 4.0.7, X-PLOR NIH 3.0.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 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 TOTAL BURIED SURFACE AREA: 340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 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 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 19 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 19 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 21 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA A 21 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 21 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 21 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 23 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 24 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 24 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 24 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 25 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 25 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 25 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 25 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 26 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 27 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT A 27 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 27 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT A 28 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 28 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 29 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 30 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 31 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 31 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 31 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 520 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 DT A 20 0.07 SIDE CHAIN REMARK 500 1 DT A 23 0.07 SIDE CHAIN REMARK 500 1 DA A 25 0.05 SIDE CHAIN REMARK 500 1 DT A 29 0.07 SIDE CHAIN REMARK 500 1 DG A 35 0.07 SIDE CHAIN REMARK 500 2 DA A 3 0.06 SIDE CHAIN REMARK 500 2 DG A 5 0.06 SIDE CHAIN REMARK 500 2 DG A 9 0.06 SIDE CHAIN REMARK 500 2 DA A 25 0.06 SIDE CHAIN REMARK 500 2 DT A 33 0.08 SIDE CHAIN REMARK 500 2 DA A 34 0.06 SIDE CHAIN REMARK 500 3 DA A 3 0.08 SIDE CHAIN REMARK 500 3 DG A 4 0.06 SIDE CHAIN REMARK 500 3 DT A 23 0.06 SIDE CHAIN REMARK 500 4 DT A 2 0.07 SIDE CHAIN REMARK 500 4 DA A 3 0.07 SIDE CHAIN REMARK 500 4 DG A 4 0.05 SIDE CHAIN REMARK 500 4 DG A 9 0.07 SIDE CHAIN REMARK 500 4 DA A 11 0.05 SIDE CHAIN REMARK 500 4 DT A 20 0.07 SIDE CHAIN REMARK 500 4 DA A 25 0.05 SIDE CHAIN REMARK 500 5 DA A 3 0.06 SIDE CHAIN REMARK 500 5 DT A 20 0.07 SIDE CHAIN REMARK 500 6 DA A 3 0.08 SIDE CHAIN REMARK 500 6 DT A 10 0.08 SIDE CHAIN REMARK 500 6 DA A 11 0.09 SIDE CHAIN REMARK 500 6 DT A 26 0.08 SIDE CHAIN REMARK 500 6 DT A 28 0.09 SIDE CHAIN REMARK 500 7 DA A 11 0.07 SIDE CHAIN REMARK 500 7 DT A 20 0.08 SIDE CHAIN REMARK 500 7 DT A 26 0.07 SIDE CHAIN REMARK 500 8 DA A 3 0.08 SIDE CHAIN REMARK 500 8 DG A 4 0.05 SIDE CHAIN REMARK 500 8 DT A 20 0.07 SIDE CHAIN REMARK 500 8 DT A 23 0.08 SIDE CHAIN REMARK 500 9 DT A 20 0.07 SIDE CHAIN REMARK 500 9 DT A 23 0.07 SIDE CHAIN REMARK 500 10 DA A 3 0.08 SIDE CHAIN REMARK 500 10 DG A 4 0.08 SIDE CHAIN REMARK 500 10 DG A 9 0.07 SIDE CHAIN REMARK 500 10 DA A 11 0.08 SIDE CHAIN REMARK 500 10 DT A 20 0.06 SIDE CHAIN REMARK 500 10 DT A 26 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34664 RELATED DB: BMRB REMARK 900 PARALLEL Q-D HYBRID WITH 3' DUPLEX STEM-LOOP AS A LATERAL SNAPBACK REMARK 900 LOOP DBREF 7PNE A 1 36 PDB 7PNE 7PNE 1 36 SEQRES 1 A 36 THM DT DA DG DG DT DG DG DG DT DA DG DG SEQRES 2 A 36 DG DT DG DG DG DC DT DA DG DT DC DA DT SEQRES 3 A 36 DT DT DT DG DA DC DT DA DG DG HET THM A 1 30 HETNAM THM THYMIDINE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE FORMUL 1 THM C10 H14 N2 O5 LINK O3' THM A 1 P DT A 2 1555 1555 1.61 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 HETATM 1 O5' THM A 1 26.282 13.694 30.792 1.00 0.00 O HETATM 2 C5' THM A 1 26.709 13.178 29.532 1.00 0.00 C HETATM 3 C4' THM A 1 27.406 14.236 28.658 1.00 0.00 C HETATM 4 O4' THM A 1 26.522 15.321 28.397 1.00 0.00 O HETATM 5 C3' THM A 1 28.664 14.849 29.311 1.00 0.00 C HETATM 6 O3' THM A 1 29.813 14.815 28.476 1.00 0.00 O HETATM 7 C2' THM A 1 28.275 16.312 29.501 1.00 0.00 C HETATM 8 C1' THM A 1 27.322 16.486 28.320 1.00 0.00 C HETATM 9 N1 THM A 1 26.474 17.713 28.289 1.00 0.00 N HETATM 10 C2 THM A 1 25.925 18.057 27.043 1.00 0.00 C HETATM 11 O2 THM A 1 26.166 17.460 25.992 1.00 0.00 O HETATM 12 N3 THM A 1 25.072 19.135 27.011 1.00 0.00 N HETATM 13 C4 THM A 1 24.717 19.908 28.091 1.00 0.00 C HETATM 14 O4 THM A 1 23.917 20.825 27.916 1.00 0.00 O HETATM 15 C5 THM A 1 25.358 19.536 29.351 1.00 0.00 C HETATM 16 C5M THM A 1 25.078 20.333 30.611 1.00 0.00 C HETATM 17 C6 THM A 1 26.201 18.471 29.416 1.00 0.00 C HETATM 18 HO5' THM A 1 25.651 14.427 30.636 1.00 0.00 H HETATM 19 H5'1 THM A 1 25.849 12.788 28.984 1.00 0.00 H HETATM 20 H5'2 THM A 1 27.405 12.353 29.696 1.00 0.00 H HETATM 21 H4' THM A 1 27.677 13.777 27.707 1.00 0.00 H HETATM 22 H3' THM A 1 28.876 14.384 30.277 1.00 0.00 H HETATM 23 H2'1 THM A 1 27.761 16.416 30.456 1.00 0.00 H HETATM 24 H2'2 THM A 1 29.130 16.986 29.432 1.00 0.00 H HETATM 25 H1' THM A 1 27.919 16.452 27.401 1.00 0.00 H HETATM 26 HN3 THM A 1 24.700 19.392 26.115 1.00 0.00 H HETATM 27 HM51 THM A 1 25.626 21.268 30.555 1.00 0.00 H HETATM 28 HM52 THM A 1 25.378 19.783 31.503 1.00 0.00 H HETATM 29 HM53 THM A 1 24.013 20.561 30.676 1.00 0.00 H HETATM 30 H6 THM A 1 26.675 18.241 30.361 1.00 0.00 H