HEADER UNKNOWN FUNCTION 03-JUL-18 6GZ7 TITLE POLYAMIDE - DNA COMPLEX NMR STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS POLYAMIDE DNA COMPLEX, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR K.AMAN REVDAT 4 23-JUN-21 6GZ7 1 REMARK REVDAT 3 08-MAY-19 6GZ7 1 REMARK REVDAT 2 06-MAR-19 6GZ7 1 JRNL REVDAT 1 28-NOV-18 6GZ7 0 JRNL AUTH K.AMAN,G.PADRONI,J.A.PARKINSON,T.WELTE,G.A.BURLEY JRNL TITL STRUCTURAL AND KINETIC PROFILING OF ALLOSTERIC MODULATION OF JRNL TITL 2 DUPLEX DNA INDUCED BY DNA-BINDING POLYAMIDE ANALOGUES. JRNL REF CHEMISTRY V. 25 2757 2019 JRNL REFN ISSN 1521-3765 JRNL PMID 30407668 JRNL DOI 10.1002/CHEM.201805338 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: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 310 NOE DISTANCE RESTRAINTS REMARK 4 REMARK 4 6GZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200010375. 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 : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.26 MM DNA (5' REMARK 210 -D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 0.24 MM POLYAMIDE REMARK 210 (PA9), 90% H2O/10% D2O; 1.26 MM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP* REMARK 210 CP*AP*TP*CP*G)-3'), 0.24 MM POLYAMIDE (PA9), 99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-11 REMARK 465 RES C SSSEQI REMARK 465 PA9 A 1 REMARK 465 PA9 B 13 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-11 REMARK 470 RES CSSEQI ATOMS REMARK 470 DC A 2 P OP1 OP2 REMARK 470 DC B 14 P OP1 OP2 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 6 DC B 14 C5' DC B 14 C4' 0.045 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 8 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 10 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 10 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC A 12 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 15 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 16 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 16 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 20 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA B 20 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 21 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC B 21 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA B 22 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 22 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT B 23 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 23 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC B 24 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 25 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DA A 8 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DA A 8 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 431 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 6 0.06 SIDE CHAIN REMARK 500 1 DT A 7 0.15 SIDE CHAIN REMARK 500 1 DA A 8 0.09 SIDE CHAIN REMARK 500 1 DG B 15 0.07 SIDE CHAIN REMARK 500 1 DG B 18 0.11 SIDE CHAIN REMARK 500 1 DT B 19 0.11 SIDE CHAIN REMARK 500 2 DG A 6 0.10 SIDE CHAIN REMARK 500 2 DT A 7 0.13 SIDE CHAIN REMARK 500 2 DA A 8 0.06 SIDE CHAIN REMARK 500 2 DG B 18 0.09 SIDE CHAIN REMARK 500 2 DT B 19 0.09 SIDE CHAIN REMARK 500 3 DA A 4 0.07 SIDE CHAIN REMARK 500 3 DG A 6 0.07 SIDE CHAIN REMARK 500 3 DT A 7 0.14 SIDE CHAIN REMARK 500 3 DA A 8 0.08 SIDE CHAIN REMARK 500 3 DT A 11 0.07 SIDE CHAIN REMARK 500 3 DG B 18 0.13 SIDE CHAIN REMARK 500 3 DT B 19 0.12 SIDE CHAIN REMARK 500 4 DG A 6 0.12 SIDE CHAIN REMARK 500 4 DT A 7 0.13 SIDE CHAIN REMARK 500 4 DA A 8 0.07 SIDE CHAIN REMARK 500 4 DG B 18 0.11 SIDE CHAIN REMARK 500 4 DT B 19 0.10 SIDE CHAIN REMARK 500 5 DA A 4 0.05 SIDE CHAIN REMARK 500 5 DG A 6 0.09 SIDE CHAIN REMARK 500 5 DT A 7 0.14 SIDE CHAIN REMARK 500 5 DA A 8 0.07 SIDE CHAIN REMARK 500 5 DG B 18 0.11 SIDE CHAIN REMARK 500 5 DT B 19 0.10 SIDE CHAIN REMARK 500 6 DG A 3 0.06 SIDE CHAIN REMARK 500 6 DA A 4 0.08 SIDE CHAIN REMARK 500 6 DG A 6 0.07 SIDE CHAIN REMARK 500 6 DT A 7 0.11 SIDE CHAIN REMARK 500 6 DA A 8 0.06 SIDE CHAIN REMARK 500 6 DC B 14 0.06 SIDE CHAIN REMARK 500 6 DG B 15 0.06 SIDE CHAIN REMARK 500 6 DG B 18 0.11 SIDE CHAIN REMARK 500 6 DT B 19 0.10 SIDE CHAIN REMARK 500 6 DT B 23 0.07 SIDE CHAIN REMARK 500 6 DC B 24 0.10 SIDE CHAIN REMARK 500 7 DA A 4 0.08 SIDE CHAIN REMARK 500 7 DG A 6 0.11 SIDE CHAIN REMARK 500 7 DT A 7 0.12 SIDE CHAIN REMARK 500 7 DA A 8 0.07 SIDE CHAIN REMARK 500 7 DG B 15 0.06 SIDE CHAIN REMARK 500 7 DG B 18 0.09 SIDE CHAIN REMARK 500 7 DT B 19 0.08 SIDE CHAIN REMARK 500 8 DA A 4 0.06 SIDE CHAIN REMARK 500 8 DG A 6 0.09 SIDE CHAIN REMARK 500 8 DT A 7 0.13 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 76 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 FGW A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34296 RELATED DB: BMRB REMARK 900 POLYAMIDE - DNA COMPLEX NMR STRUCTURE DBREF 6GZ7 A 1 13 PDB 6GZ7 6GZ7 1 13 DBREF 6GZ7 B 13 25 PDB 6GZ7 6GZ7 13 25 SEQRES 1 A 13 PA9 DC DG DA DT DG DT DA DC DA DT DC DG SEQRES 1 B 13 PA9 DC DG DA DT DG DT DA DC DA DT DC DG HET FGW A 101 167 HETNAM FGW DIMETHYL-[3-[3-[[1-METHYL-4-[[1-METHYL-4-[[1-METHYL-4- HETNAM 2 FGW [[1-METHYL-4-[4-[[1-METHYL-4-[[1-METHYL-4-[[1-METHYL- HETNAM 3 FGW 4-[(1-PROPAN-2-YLIMIDAZOL-2-YL)CARBONYLAMINO]PYRROL-2- HETNAM 4 FGW YL]CARBONYLAMINO]PYRROL-2-YL]CARBONYLAMINO]PYRROL-2- HETNAM 5 FGW YL]CARBONYLAMINO]BUTANOYLAMINO]IMIDAZOL-2- HETNAM 6 FGW YL]CARBONYLAMINO]PYRROL-2-YL]CARBONYLAMINO]PYRROL-2- HETNAM 7 FGW YL]CARBONYLAMINO]PYRROL-2- HETNAM 8 FGW YL]CARBONYLAMINO]PROPANOYLAMINO]PROPYL]AZANIUM FORMUL 3 FGW C60 H76 N21 O10 1+ SITE 1 AC1 16 DT A 5 DG A 6 DT A 7 DA A 8 SITE 2 AC1 16 DC A 9 DA A 10 DT A 11 DT B 17 SITE 3 AC1 16 DG B 18 DT B 19 DA B 20 DC B 21 SITE 4 AC1 16 DA B 22 DT B 23 DC B 24 DG B 25 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