HEADER DNA 20-DEC-17 6FC9 TITLE THE 1,8-BIS(AMINOMETHYL)ANTHRACENE AND QUADRUPLEX-DUPLEX JUNCTION TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS QUADRUPLEX, JUNCTION, NON CANONICAL DNA STRUCUTE, LIGAND-DNA COMPLEX, KEYWDS 2 DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.SANTANA,I.SERRANO,L.MONTALVILLO-JIMENEZ,F.CORZANA,A.BASTIDA, AUTHOR 2 J.JIMENEZ-BARBERO,C.GONZALEZ,J.L.ASENSIO REVDAT 5 19-JUN-24 6FC9 1 REMARK REVDAT 4 14-JUN-23 6FC9 1 REMARK REVDAT 3 07-APR-21 6FC9 1 JRNL REMARK REVDAT 2 08-MAY-19 6FC9 1 REMARK REVDAT 1 10-APR-19 6FC9 0 JRNL AUTH L.DIAZ-CASADO,I.SERRANO-CHACON,L.MONTALVILLO-JIMENEZ, JRNL AUTH 2 F.CORZANA,A.BASTIDA,A.G.SANTANA,C.GONZALEZ,J.L.ASENSIO JRNL TITL DE NOVO DESIGN OF SELECTIVE QUADRUPLEX-DUPLEX JUNCTION JRNL TITL 2 LIGANDS AND STRUCTURAL CHARACTERISATION OF THEIR BINDING JRNL TITL 3 MODE: TARGETING THE G4 HOT-SPOT. JRNL REF CHEMISTRY 2020 JRNL REFN ISSN 0947-6539 JRNL PMID 33368678 JRNL DOI 10.1002/CHEM.202005026 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007532. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 293 REMARK 210 PH : 6.9; 6.9 REMARK 210 IONIC STRENGTH : 20 MM KPI 20 MM KCL; 20 MM KPI REMARK 210 20 MM KCL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM NA JQ2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY 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 : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA A 12 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 14 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DA A 15 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 15 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 17 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC A 20 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DC A 20 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DG A 23 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 27 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 12 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DC A 14 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 15 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 16 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 16 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 17 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DC A 20 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 20 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DG A 21 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 288 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 5 0.08 SIDE CHAIN REMARK 500 1 DA A 12 0.09 SIDE CHAIN REMARK 500 1 DC A 14 0.10 SIDE CHAIN REMARK 500 1 DT A 16 0.07 SIDE CHAIN REMARK 500 1 DC A 18 0.06 SIDE CHAIN REMARK 500 1 DG A 23 0.08 SIDE CHAIN REMARK 500 1 DT A 25 0.08 SIDE CHAIN REMARK 500 1 DG A 26 0.08 SIDE CHAIN REMARK 500 1 DG A 27 0.06 SIDE CHAIN REMARK 500 2 DC A 7 0.12 SIDE CHAIN REMARK 500 2 DG A 8 0.07 SIDE CHAIN REMARK 500 2 DA A 12 0.07 SIDE CHAIN REMARK 500 2 DC A 14 0.11 SIDE CHAIN REMARK 500 2 DT A 16 0.08 SIDE CHAIN REMARK 500 2 DG A 19 0.07 SIDE CHAIN REMARK 500 2 DT A 25 0.09 SIDE CHAIN REMARK 500 2 DG A 26 0.06 SIDE CHAIN REMARK 500 3 DG A 1 0.07 SIDE CHAIN REMARK 500 3 DC A 7 0.07 SIDE CHAIN REMARK 500 3 DG A 8 0.05 SIDE CHAIN REMARK 500 3 DA A 12 0.10 SIDE CHAIN REMARK 500 3 DC A 14 0.10 SIDE CHAIN REMARK 500 3 DG A 19 0.06 SIDE CHAIN REMARK 500 3 DG A 23 0.08 SIDE CHAIN REMARK 500 3 DT A 25 0.09 SIDE CHAIN REMARK 500 3 DG A 26 0.07 SIDE CHAIN REMARK 500 3 DG A 27 0.06 SIDE CHAIN REMARK 500 4 DG A 1 0.06 SIDE CHAIN REMARK 500 4 DA A 12 0.06 SIDE CHAIN REMARK 500 4 DC A 14 0.07 SIDE CHAIN REMARK 500 4 DA A 15 0.07 SIDE CHAIN REMARK 500 4 DC A 18 0.06 SIDE CHAIN REMARK 500 5 DG A 6 0.06 SIDE CHAIN REMARK 500 5 DG A 8 0.07 SIDE CHAIN REMARK 500 5 DA A 12 0.07 SIDE CHAIN REMARK 500 5 DC A 14 0.09 SIDE CHAIN REMARK 500 5 DA A 15 0.07 SIDE CHAIN REMARK 500 5 DT A 16 0.07 SIDE CHAIN REMARK 500 5 DC A 18 0.07 SIDE CHAIN REMARK 500 5 DG A 19 0.07 SIDE CHAIN REMARK 500 5 DT A 25 0.08 SIDE CHAIN REMARK 500 5 DG A 26 0.10 SIDE CHAIN REMARK 500 5 DG A 27 0.06 SIDE CHAIN REMARK 500 6 DG A 8 0.06 SIDE CHAIN REMARK 500 6 DC A 14 0.07 SIDE CHAIN REMARK 500 6 DA A 15 0.07 SIDE CHAIN REMARK 500 6 DT A 16 0.06 SIDE CHAIN REMARK 500 6 DC A 18 0.07 SIDE CHAIN REMARK 500 6 DG A 22 0.05 SIDE CHAIN REMARK 500 6 DT A 25 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 80 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D5B A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34221 RELATED DB: BMRB REMARK 900 THE 1,8-BIS(AMINOMETHYL)ANTHRACENE AND QUADRUPLEX-DUPLEX JUNCTION REMARK 900 COMPLEX DBREF 6FC9 A 1 27 PDB 6FC9 6FC9 1 27 SEQRES 1 A 27 DG DG DT DT DG DG DC DG DC DG DA DA DG SEQRES 2 A 27 DC DA DT DT DC DG DC DG DG DG DT DT DG SEQRES 3 A 27 DG HET D5B A 101 36 HETNAM D5B [8-(AZANIUMYLMETHYL)ANTHRACEN-1-YL]METHYLAZANIUM FORMUL 2 D5B C16 H18 N2 2+ SITE 1 AC1 6 DG A 1 DG A 6 DC A 20 DG A 21 SITE 2 AC1 6 DG A 22 DG A 27 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