HEADER DNA 06-SEP-21 7PNG
TITLE SOLUTION STRUCTURE OF 1:1 COMPLEX OF AN INDOLOQUINOLINE DERIVATIVE
TITLE 2 SYUIQ-5 TO PARALLEL QUADRUPLEX-DUPLEX (Q-D) HYBRID
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (37-MER);
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, SYUIQ-5,
KEYWDS 2 COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR Y.M.VIANNEY,K.WEISZ
REVDAT 5 19-JUN-24 7PNG 1 REMARK
REVDAT 4 16-FEB-22 7PNG 1 JRNL
REVDAT 3 09-FEB-22 7PNG 1 JRNL
REVDAT 2 19-JAN-22 7PNG 1 JRNL
REVDAT 1 29-DEC-21 7PNG 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 7PNG 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_1292118020.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
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 DQF
REMARK 210 -COSY; 2D 1H-1H NOESY; 2D 1H-1H
REMARK 210 TOCSY
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: 430 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6580 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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. = 3.5 DEGREES
REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 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. = 4.1 DEGREES
REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DC A 19 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DA A 21 O4' - C1' - N9 ANGL. DEV. = 2.0 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. = -5.6 DEGREES
REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DT A 23 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DC A 24 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DC A 24 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DA A 25 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DA A 25 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 DA A 25 C5 - C6 - N1 ANGL. DEV. = 3.5 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. = -3.9 DEGREES
REMARK 500 1 DT A 27 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT A 27 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DT A 28 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DT A 29 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DG A 30 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 DA A 31 C4 - C5 - C6 ANGL. DEV. = -3.1 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. = -5.2 DEGREES
REMARK 500 1 DC A 32 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DC A 32 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 521 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 16 0.07 SIDE CHAIN
REMARK 500 1 DG A 18 0.06 SIDE CHAIN
REMARK 500 1 DA A 25 0.06 SIDE CHAIN
REMARK 500 1 DT A 33 0.08 SIDE CHAIN
REMARK 500 1 DG A 36 0.10 SIDE CHAIN
REMARK 500 2 DA A 3 0.07 SIDE CHAIN
REMARK 500 2 DG A 4 0.07 SIDE CHAIN
REMARK 500 2 DC A 19 0.07 SIDE CHAIN
REMARK 500 2 DA A 21 0.07 SIDE CHAIN
REMARK 500 2 DA A 25 0.09 SIDE CHAIN
REMARK 500 2 DT A 27 0.08 SIDE CHAIN
REMARK 500 2 DT A 33 0.07 SIDE CHAIN
REMARK 500 2 DG A 36 0.06 SIDE CHAIN
REMARK 500 3 DA A 25 0.07 SIDE CHAIN
REMARK 500 3 DT A 33 0.06 SIDE CHAIN
REMARK 500 3 DG A 36 0.07 SIDE CHAIN
REMARK 500 4 DA A 25 0.07 SIDE CHAIN
REMARK 500 4 DT A 26 0.07 SIDE CHAIN
REMARK 500 4 DG A 36 0.12 SIDE CHAIN
REMARK 500 5 DG A 5 0.05 SIDE CHAIN
REMARK 500 5 DT A 26 0.07 SIDE CHAIN
REMARK 500 5 DT A 27 0.07 SIDE CHAIN
REMARK 500 5 DG A 36 0.11 SIDE CHAIN
REMARK 500 6 DG A 5 0.06 SIDE CHAIN
REMARK 500 7 DG A 9 0.08 SIDE CHAIN
REMARK 500 7 DA A 25 0.06 SIDE CHAIN
REMARK 500 7 DG A 35 0.09 SIDE CHAIN
REMARK 500 8 DT A 2 0.06 SIDE CHAIN
REMARK 500 8 DG A 5 0.06 SIDE CHAIN
REMARK 500 8 DG A 7 0.09 SIDE CHAIN
REMARK 500 9 DA A 3 0.05 SIDE CHAIN
REMARK 500 9 DT A 29 0.08 SIDE CHAIN
REMARK 500 9 DT A 33 0.07 SIDE CHAIN
REMARK 500 9 DG A 36 0.07 SIDE CHAIN
REMARK 500 10 DA A 3 0.06 SIDE CHAIN
REMARK 500 10 DG A 4 0.06 SIDE CHAIN
REMARK 500 10 DG A 13 0.06 SIDE CHAIN
REMARK 500 10 DA A 25 0.07 SIDE CHAIN
REMARK 500 10 DT A 29 0.06 SIDE CHAIN
REMARK 500 10 DT A 33 0.07 SIDE CHAIN
REMARK 500 10 DG A 36 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 34665 RELATED DB: BMRB
REMARK 900 SOLUTION STRUCTURE OF 1:1 COMPLEX OF AN INDOLOQUINOLINE DERIVATIVE
REMARK 900 SYUIQ-5 TO PARALLEL QUADRUPLEX-DUPLEX (Q-D) HYBRID
DBREF 7PNG A 1 36 PDB 7PNG 7PNG 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
HET 7V5 A 101 48
HETNAM THM THYMIDINE
HETNAM 7V5 ~{N}-(5~{H}-INDOLO[3,2-B]QUINOLIN-11-YL)-~{N}',~{N}'-
HETNAM 2 7V5 DIMETHYL-PROPANE-1,3-DIAMINE
HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
FORMUL 1 THM C10 H14 N2 O5
FORMUL 2 7V5 C20 H24 N4 2+
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 28.014 37.803 18.439 1.00 0.00 O
HETATM 2 C5' THM A 1 26.806 37.099 18.166 1.00 0.00 C
HETATM 3 C4' THM A 1 25.778 37.942 17.396 1.00 0.00 C
HETATM 4 O4' THM A 1 25.464 39.111 18.150 1.00 0.00 O
HETATM 5 C3' THM A 1 26.320 38.396 16.030 1.00 0.00 C
HETATM 6 O3' THM A 1 25.335 38.305 15.009 1.00 0.00 O
HETATM 7 C2' THM A 1 26.633 39.868 16.266 1.00 0.00 C
HETATM 8 C1' THM A 1 25.524 40.214 17.269 1.00 0.00 C
HETATM 9 N1 THM A 1 25.666 41.512 17.995 1.00 0.00 N
HETATM 10 C2 THM A 1 24.573 42.394 17.950 1.00 0.00 C
HETATM 11 O2 THM A 1 23.461 42.098 17.509 1.00 0.00 O
HETATM 12 N3 THM A 1 24.783 43.673 18.411 1.00 0.00 N
HETATM 13 C4 THM A 1 25.972 44.169 18.897 1.00 0.00 C
HETATM 14 O4 THM A 1 26.030 45.358 19.214 1.00 0.00 O
HETATM 15 C5 THM A 1 27.053 43.187 18.983 1.00 0.00 C
HETATM 16 C5M THM A 1 28.412 43.602 19.523 1.00 0.00 C
HETATM 17 C6 THM A 1 26.862 41.904 18.570 1.00 0.00 C
HETATM 18 HO5' THM A 1 28.724 37.426 17.870 1.00 0.00 H
HETATM 19 H5'1 THM A 1 26.350 36.784 19.101 1.00 0.00 H
HETATM 20 H5'2 THM A 1 27.030 36.202 17.586 1.00 0.00 H
HETATM 21 H4' THM A 1 24.877 37.345 17.243 1.00 0.00 H
HETATM 22 H3' THM A 1 27.217 37.825 15.777 1.00 0.00 H
HETATM 23 H2'1 THM A 1 27.632 39.957 16.684 1.00 0.00 H
HETATM 24 H2'2 THM A 1 26.544 40.454 15.350 1.00 0.00 H
HETATM 25 H1' THM A 1 24.590 40.228 16.699 1.00 0.00 H
HETATM 26 HN3 THM A 1 24.004 44.304 18.374 1.00 0.00 H
HETATM 27 HM51 THM A 1 28.847 44.352 18.860 1.00 0.00 H
HETATM 28 HM52 THM A 1 29.088 42.749 19.595 1.00 0.00 H
HETATM 29 HM53 THM A 1 28.294 44.052 20.508 1.00 0.00 H
HETATM 30 H6 THM A 1 27.658 41.184 18.694 1.00 0.00 H