HEADER DNA 15-SEP-19 6KXZ TITLE HUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 EPIRUBICIN TITLE 2 (EPI) MOLECULES COMPND MOL_ID: 1; COMPND 2 MOLECULE: [TTAGGGT]4-EPI-COMPLEX; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DT5 = THY AT 5' TER DT3 = THY AT 3' TER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, EPIRUBICIN, EPIADRIAMYCIN, DNA EXPDTA SOLUTION NMR NUMMDL 15 MDLTYP CHAIN A, B, C, D, L AUTHOR R.BARTHWAL,S.RAJE,K.PANDAV REVDAT 3 29-SEP-21 6KXZ 1 JRNL REVDAT 2 03-FEB-21 6KXZ 1 SEQRES REVDAT 1 16-SEP-20 6KXZ 0 JRNL AUTH R.BARTHWAL,S.RAJE,K.PANDAV JRNL TITL STRUCTURAL BASIS FOR STABILIZATION OF HUMAN TELOMERIC JRNL TITL 2 G-QUADRUPLEX [D-(TTAGGGT)] 4 BY ANTICANCER DRUG EPIRUBICIN. JRNL REF BIOORG.MED.CHEM. V. 28 15761 2020 JRNL REFN ESSN 1464-3391 JRNL PMID 32992248 JRNL DOI 10.1016/J.BMC.2020.115761 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 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KXZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013821. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.11 MM (DT5)TAGGG(DT3), 2.22 MM REMARK 210 EPIRUBICIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 35 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT B 8 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT B 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA B 10 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 10 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 10 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT C 15 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT C 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT C 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA C 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA C 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA C 17 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA C 17 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG C 19 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT C 21 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT D 23 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT D 23 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA D 24 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA D 24 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA D 24 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA D 24 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG D 25 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG D 26 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT D 28 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT D 28 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 8 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT B 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA B 10 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA B 10 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA B 10 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 547 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 2 0.06 SIDE CHAIN REMARK 500 2 DG C 20 0.06 SIDE CHAIN REMARK 500 2 DA D 24 0.05 SIDE CHAIN REMARK 500 3 DT A 2 0.07 SIDE CHAIN REMARK 500 4 DA A 3 0.07 SIDE CHAIN REMARK 500 4 DG A 6 0.06 SIDE CHAIN REMARK 500 4 DT A 7 0.06 SIDE CHAIN REMARK 500 4 DA C 17 0.09 SIDE CHAIN REMARK 500 5 DG B 11 0.07 SIDE CHAIN REMARK 500 5 DG D 25 0.08 SIDE CHAIN REMARK 500 5 DG D 26 0.06 SIDE CHAIN REMARK 500 6 DA C 17 0.06 SIDE CHAIN REMARK 500 6 DG D 25 0.05 SIDE CHAIN REMARK 500 7 DT C 16 0.08 SIDE CHAIN REMARK 500 7 DA C 17 0.09 SIDE CHAIN REMARK 500 8 DT B 14 0.06 SIDE CHAIN REMARK 500 8 DA D 24 0.07 SIDE CHAIN REMARK 500 9 DA A 3 0.06 SIDE CHAIN REMARK 500 9 DG C 20 0.07 SIDE CHAIN REMARK 500 10 DT A 1 0.07 SIDE CHAIN REMARK 500 10 DA C 17 0.06 SIDE CHAIN REMARK 500 10 DG D 25 0.05 SIDE CHAIN REMARK 500 11 DA D 24 0.06 SIDE CHAIN REMARK 500 13 DA C 17 0.06 SIDE CHAIN REMARK 500 13 DG C 18 0.07 SIDE CHAIN REMARK 500 13 DG D 25 0.05 SIDE CHAIN REMARK 500 14 DA A 3 0.06 SIDE CHAIN REMARK 500 15 DA A 3 0.06 SIDE CHAIN REMARK 500 15 DA D 24 0.06 SIDE CHAIN 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 DM6 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DM6 A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36287 RELATED DB: BMRB REMARK 900 HUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 REMARK 900 EPIRUBICIN (DM2) MOLECULES DBREF 6KXZ A 1 7 PDB 6KXZ 6KXZ 1 7 DBREF 6KXZ B 8 14 PDB 6KXZ 6KXZ 8 14 DBREF 6KXZ C 15 21 PDB 6KXZ 6KXZ 15 21 DBREF 6KXZ D 22 28 PDB 6KXZ 6KXZ 22 28 SEQRES 1 A 7 DT DT DA DG DG DG DT SEQRES 1 B 7 DT DT DA DG DG DG DT SEQRES 1 C 7 DT DT DA DG DG DG DT SEQRES 1 D 7 DT DT DA DG DG DG DT HET DM6 A 101 68 HET DM6 A 102 68 HETNAM DM6 4'-EPIDOXORUBICIN HETSYN DM6 4'-EPIADRIAMYCIN FORMUL 5 DM6 2(C27 H30 N O11 1+) SITE 1 AC1 3 DA A 3 DG A 4 DT D 22 SITE 1 AC2 2 DG A 6 DT A 7 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15