HEADER DNA BINDING PROTEIN 05-JUL-17 5ODF TITLE NTME POLYAMIDE IN COMPLEX WITH 5'CGATGTACATCG3'- HAIRPIN POLYAMIDES TITLE 2 STUDIES 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: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS DNA, MINOR GROOVE BINDERS, HAIRPIN POLYAMIDES, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.PADRONI,J.PARKINSON,G.A.BURLEY REVDAT 4 14-JUN-23 5ODF 1 REMARK REVDAT 3 08-MAY-19 5ODF 1 REMARK REVDAT 2 24-JAN-18 5ODF 1 JRNL REVDAT 1 20-DEC-17 5ODF 0 JRNL AUTH G.PADRONI,J.A.PARKINSON,K.R.FOX,G.A.BURLEY JRNL TITL STRUCTURAL BASIS OF DNA DUPLEX DISTORTION INDUCED BY JRNL TITL 2 THIAZOLE-CONTAINING HAIRPIN POLYAMIDES. JRNL REF NUCLEIC ACIDS RES. V. 46 42 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29194552 JRNL DOI 10.1093/NAR/GKX1211 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), CASE, DARDEN, REMARK 3 CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND REMARK 3 KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ODF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005609. 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 PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.3 NM DNA (5' REMARK 210 -D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 MM PA6, 90% H2O/ REMARK 210 10% D2O; 1.3 MM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3' REMARK 210 ), 1.3 MM PA6, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-13C HSQC; 1H-31P COSY; 2D 1H- REMARK 210 1H NOESY 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, MARDIGRAS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NA 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: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4740 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 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 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 8 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 8 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 17 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA B 21 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DA B 21 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 21 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT B 22 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA A 7 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC A 8 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 8 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 391 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 DA A 3 0.08 SIDE CHAIN REMARK 500 1 DG A 5 0.08 SIDE CHAIN REMARK 500 1 DT A 6 0.12 SIDE CHAIN REMARK 500 1 DA A 7 0.10 SIDE CHAIN REMARK 500 1 DA A 9 0.05 SIDE CHAIN REMARK 500 1 DA B 15 0.05 SIDE CHAIN REMARK 500 1 DG B 17 0.06 SIDE CHAIN REMARK 500 1 DT B 18 0.10 SIDE CHAIN REMARK 500 2 DA A 3 0.09 SIDE CHAIN REMARK 500 2 DG A 5 0.08 SIDE CHAIN REMARK 500 2 DT A 6 0.11 SIDE CHAIN REMARK 500 2 DA A 7 0.07 SIDE CHAIN REMARK 500 2 DA A 9 0.07 SIDE CHAIN REMARK 500 2 DT B 18 0.12 SIDE CHAIN REMARK 500 3 DA A 3 0.09 SIDE CHAIN REMARK 500 3 DT A 4 0.07 SIDE CHAIN REMARK 500 3 DG A 5 0.12 SIDE CHAIN REMARK 500 3 DT A 6 0.12 SIDE CHAIN REMARK 500 3 DA A 7 0.10 SIDE CHAIN REMARK 500 3 DC A 11 0.09 SIDE CHAIN REMARK 500 3 DG B 17 0.07 SIDE CHAIN REMARK 500 3 DT B 18 0.12 SIDE CHAIN REMARK 500 4 DA A 3 0.08 SIDE CHAIN REMARK 500 4 DG A 5 0.09 SIDE CHAIN REMARK 500 4 DT A 6 0.12 SIDE CHAIN REMARK 500 4 DA A 7 0.07 SIDE CHAIN REMARK 500 4 DA A 9 0.06 SIDE CHAIN REMARK 500 4 DT B 18 0.11 SIDE CHAIN REMARK 500 5 DG A 5 0.10 SIDE CHAIN REMARK 500 5 DT A 6 0.14 SIDE CHAIN REMARK 500 5 DA A 7 0.07 SIDE CHAIN REMARK 500 5 DA A 9 0.06 SIDE CHAIN REMARK 500 5 DC A 11 0.06 SIDE CHAIN REMARK 500 5 DA B 15 0.05 SIDE CHAIN REMARK 500 5 DG B 17 0.05 SIDE CHAIN REMARK 500 5 DT B 18 0.12 SIDE CHAIN REMARK 500 5 DA B 19 0.05 SIDE CHAIN REMARK 500 5 DA B 21 0.05 SIDE CHAIN REMARK 500 6 DA A 3 0.08 SIDE CHAIN REMARK 500 6 DG A 5 0.07 SIDE CHAIN REMARK 500 6 DT A 6 0.07 SIDE CHAIN REMARK 500 6 DA A 7 0.10 SIDE CHAIN REMARK 500 6 DA A 9 0.09 SIDE CHAIN REMARK 500 6 DG B 17 0.07 SIDE CHAIN REMARK 500 6 DT B 18 0.07 SIDE CHAIN REMARK 500 7 DA A 3 0.09 SIDE CHAIN REMARK 500 7 DG A 5 0.11 SIDE CHAIN REMARK 500 7 DT A 6 0.12 SIDE CHAIN REMARK 500 7 DA A 7 0.08 SIDE CHAIN REMARK 500 7 DA A 9 0.07 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 CWN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DCZ B 13 and DG B REMARK 800 14 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34157 RELATED DB: BMRB REMARK 900 NTME POLYAMIDE IN COMPLEX WITH 5'CGATGTACATCG3'- HAIRPIN POLYAMIDES REMARK 900 STUDIES DBREF 5ODF A 1 12 PDB 5ODF 5ODF 1 12 DBREF 5ODF B 13 24 PDB 5ODF 5ODF 13 24 SEQRES 1 A 12 DCZ DG DA DT DG DT DA DC DA DT DC DG SEQRES 1 B 12 DCZ DG DA DT DG DT DA DC DA DT DC DG HET DCZ A 1 28 HET DCZ B 13 28 HET CWN A 101 160 HETNAM DCZ 2'-DEOXYCYTIDINE HETNAM CWN NTME POLYAMIDE FORMUL 1 DCZ 2(C9 H13 N3 O4) FORMUL 3 CWN C58 H71 N20 O10 S 1+ LINK O3' DCZ A 1 P DG A 2 1555 1555 1.61 LINK O3' DCZ B 13 P DG B 14 1555 1555 1.62 SITE 1 AC1 16 DG A 2 DA A 3 DT A 4 DG A 5 SITE 2 AC1 16 DT A 6 DA A 7 DC A 8 DA A 9 SITE 3 AC1 16 DT A 10 DG B 17 DT B 18 DA B 19 SITE 4 AC1 16 DC B 20 DA B 21 DT B 22 DC B 23 SITE 1 AC2 2 DC A 11 DA B 15 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 N1 DCZ A 1 30.547 8.159 23.595 1.00 0.00 N HETATM 2 C2 DCZ A 1 29.454 7.485 23.022 1.00 0.00 C HETATM 3 N3 DCZ A 1 28.185 7.758 23.419 1.00 0.00 N HETATM 4 C4 DCZ A 1 28.007 8.658 24.363 1.00 0.00 C HETATM 5 C5 DCZ A 1 29.069 9.349 25.004 1.00 0.00 C HETATM 6 C6 DCZ A 1 30.333 9.079 24.592 1.00 0.00 C HETATM 7 O2 DCZ A 1 29.603 6.632 22.141 1.00 0.00 O HETATM 8 N4 DCZ A 1 26.768 8.915 24.670 1.00 0.00 N HETATM 9 C1' DCZ A 1 31.915 7.937 23.040 1.00 0.00 C HETATM 10 C2' DCZ A 1 32.408 9.159 22.251 1.00 0.00 C HETATM 11 C3' DCZ A 1 33.518 9.746 23.122 1.00 0.00 C HETATM 12 C4' DCZ A 1 34.040 8.462 23.772 1.00 0.00 C HETATM 13 O4' DCZ A 1 32.861 7.725 24.081 1.00 0.00 O HETATM 14 O3' DCZ A 1 34.501 10.402 22.333 1.00 0.00 O HETATM 15 C5' DCZ A 1 34.929 8.675 25.014 1.00 0.00 C HETATM 16 O5' DCZ A 1 34.309 9.433 26.054 1.00 0.00 O HETATM 17 H5 DCZ A 1 28.904 10.079 25.781 1.00 0.00 H HETATM 18 H6 DCZ A 1 31.182 9.586 25.039 1.00 0.00 H HETATM 19 HN41 DCZ A 1 26.050 8.410 24.179 1.00 0.00 H HETATM 20 HN42 DCZ A 1 26.564 9.640 25.338 1.00 0.00 H HETATM 21 H1' DCZ A 1 31.912 7.069 22.373 1.00 0.00 H HETATM 22 H2'1 DCZ A 1 31.619 9.892 22.077 1.00 0.00 H HETATM 23 H2'2 DCZ A 1 32.816 8.821 21.297 1.00 0.00 H HETATM 24 H3' DCZ A 1 33.092 10.400 23.885 1.00 0.00 H HETATM 25 H4' DCZ A 1 34.617 7.908 23.028 1.00 0.00 H HETATM 26 H5'1 DCZ A 1 35.207 7.692 25.401 1.00 0.00 H HETATM 27 H5'2 DCZ A 1 35.847 9.176 24.699 1.00 0.00 H HETATM 28 HO51 DCZ A 1 34.339 10.386 25.833 1.00 0.00 H