HEADER DNA 15-SEP-06 2IDN TITLE NMR STRUCTURE OF A NEW MODIFIED THROMBIN BINDING APTAMER TITLE 2 CONTAINING A 5'-5' INVERSION OF POLARITY SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3'-D(P*GP*G*T)-5'-5'- COMPND 3 D(P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE ORIGINAL SEQUENCE (THE ONE WITHOUT SOURCE 4 INVERSION OF POLARITY) HAS BEEN SELECTED IN THE SELEX SOURCE 5 PROCESS KEYWDS INVERSION OF POLARITY, TBA, ANTICOAGULANT, DNA, QUADRUPLEX, KEYWDS 2 5'-5' EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR A.RANDAZZO,L.MARTINO,A.VIRNO,L.MAYOL,C.GIANCOLA REVDAT 2 24-FEB-09 2IDN 1 VERSN REVDAT 1 09-JAN-07 2IDN 0 JRNL AUTH L.MARTINO,A.VIRNO,A.RANDAZZO,A.VIRGILIO,V.ESPOSITO, JRNL AUTH 2 C.GIANCOLA,M.BUCCI,G.CIRINO,L.MAYOL JRNL TITL A NEW MODIFIED THROMBIN BINDING APTAMER CONTAINING JRNL TITL 2 A 5'-5' INVERSION OF POLARITY SITE. JRNL REF NUCLEIC ACIDS RES. V. 34 6653 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 17145716 JRNL DOI 10.1093/NAR/GKL915 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : ACCELRYS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 288 RESTRAINTS, 198 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 54 DIHEDRAL ANGLE RESTRAINTS, 36 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 2IDN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-06. REMARK 100 THE RCSB ID CODE IS RCSB039452. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM PHOSPHATE BUFFER K, 70 REMARK 210 MM KCL, 0.2 MM EDTA, 90% H2O, REMARK 210 10% D2O; 20 MM PHOSPHATE REMARK 210 BUFFER K, 70 MM KCL, 0.2 MM REMARK 210 EDTA, D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 1H-15N HSQC, 2D REMARK 210 TOCSY, PE-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : INSIGHT II 2005 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES, AND BY USING A 1H-15N HSQC PERFORMED REMARK 210 ON THE UNLABELED MOLECULE 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 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 1-7 REMARK 470 RES CSSEQI ATOMS REMARK 470 DT A 3 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 1 DG A 1 N1 DG A 1 C2 0.111 REMARK 500 1 DG A 1 N3 DG A 1 C4 0.095 REMARK 500 1 DG A 1 C4 DG A 1 C5 0.059 REMARK 500 1 DG A 1 C5 DG A 1 C6 0.124 REMARK 500 1 DG A 1 N7 DG A 1 C8 0.060 REMARK 500 1 DG A 1 C2 DG A 1 N2 0.068 REMARK 500 1 DG A 2 N1 DG A 2 C2 0.104 REMARK 500 1 DG A 2 N3 DG A 2 C4 0.100 REMARK 500 1 DG A 2 C4 DG A 2 C5 0.057 REMARK 500 1 DG A 2 C5 DG A 2 C6 0.131 REMARK 500 1 DG A 2 N7 DG A 2 C8 0.067 REMARK 500 1 DG A 2 C2 DG A 2 N2 0.068 REMARK 500 1 DT A 3 C4 DT A 3 C5 0.112 REMARK 500 1 DT A 3 C6 DT A 3 N1 0.115 REMARK 500 1 DT A 4 C4 DT A 4 C5 0.111 REMARK 500 1 DT A 4 C6 DT A 4 N1 0.117 REMARK 500 1 DG A 5 N1 DG A 5 C2 0.113 REMARK 500 1 DG A 5 N3 DG A 5 C4 0.091 REMARK 500 1 DG A 5 C4 DG A 5 C5 0.055 REMARK 500 1 DG A 5 C5 DG A 5 C6 0.122 REMARK 500 1 DG A 5 N7 DG A 5 C8 0.061 REMARK 500 1 DG A 5 C2 DG A 5 N2 0.064 REMARK 500 1 DG A 6 C5' DG A 6 C4' 0.045 REMARK 500 1 DG A 6 N1 DG A 6 C2 0.108 REMARK 500 1 DG A 6 N3 DG A 6 C4 0.094 REMARK 500 1 DG A 6 C4 DG A 6 C5 0.055 REMARK 500 1 DG A 6 C5 DG A 6 C6 0.135 REMARK 500 1 DG A 6 N7 DG A 6 C8 0.073 REMARK 500 1 DG A 6 C2 DG A 6 N2 0.063 REMARK 500 1 DT A 7 C4 DT A 7 C5 0.113 REMARK 500 1 DT A 7 C6 DT A 7 N1 0.114 REMARK 500 1 DG A 8 N1 DG A 8 C2 0.107 REMARK 500 1 DG A 8 N3 DG A 8 C4 0.095 REMARK 500 1 DG A 8 C4 DG A 8 C5 0.058 REMARK 500 1 DG A 8 C5 DG A 8 C6 0.132 REMARK 500 1 DG A 8 N7 DG A 8 C8 0.070 REMARK 500 1 DG A 8 C2 DG A 8 N2 0.068 REMARK 500 1 DT A 9 C4 DT A 9 C5 0.112 REMARK 500 1 DT A 9 C6 DT A 9 N1 0.116 REMARK 500 1 DG A 10 N1 DG A 10 C2 0.116 REMARK 500 1 DG A 10 N3 DG A 10 C4 0.087 REMARK 500 1 DG A 10 C4 DG A 10 C5 0.054 REMARK 500 1 DG A 10 C5 DG A 10 C6 0.132 REMARK 500 1 DG A 10 N7 DG A 10 C8 0.071 REMARK 500 1 DG A 10 C2 DG A 10 N2 0.066 REMARK 500 1 DG A 11 N1 DG A 11 C2 0.112 REMARK 500 1 DG A 11 N3 DG A 11 C4 0.096 REMARK 500 1 DG A 11 C4 DG A 11 C5 0.057 REMARK 500 1 DG A 11 C5 DG A 11 C6 0.133 REMARK 500 1 DG A 11 N7 DG A 11 C8 0.065 REMARK 500 REMARK 500 THIS ENTRY HAS 462 BOND DEVIATIONS. 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 DG A 1 OP1 - P - OP2 ANGL. DEV. = -12.0 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 1 C2 - N3 - C4 ANGL. DEV. = 11.5 DEGREES REMARK 500 1 DG A 1 N3 - C4 - C5 ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DG A 1 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 1 C4 - C5 - N7 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 1 C5 - N7 - C8 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 9.5 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DG A 1 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 1 N3 - C4 - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DG A 1 C6 - C5 - N7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 1 C5 - C6 - O6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 2 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 DG A 2 C5' - C4' - C3' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 2 C2 - N3 - C4 ANGL. DEV. = 11.8 DEGREES REMARK 500 1 DG A 2 N3 - C4 - C5 ANGL. DEV. = -11.7 DEGREES REMARK 500 1 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 2 C5 - N7 - C8 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG A 2 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 2 N3 - C4 - N9 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DG A 2 C6 - C5 - N7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 3 N1 - C2 - N3 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT A 3 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT A 4 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 4 N1 - C2 - N3 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 5 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 DG A 5 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 5 C2 - N3 - C4 ANGL. DEV. = 11.6 DEGREES REMARK 500 1 DG A 5 N3 - C4 - C5 ANGL. DEV. = -11.1 DEGREES REMARK 500 1 DG A 5 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 5 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 5 C5 - N7 - C8 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DG A 5 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 5 N3 - C4 - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DG A 5 C6 - C5 - N7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 5 C5 - C6 - O6 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DG A 6 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 955 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 1 0.10 SIDE_CHAIN REMARK 500 1 DG A 11 0.08 SIDE_CHAIN REMARK 500 1 DG A 14 0.12 SIDE_CHAIN REMARK 500 2 DG A 1 0.13 SIDE_CHAIN REMARK 500 2 DG A 6 0.07 SIDE_CHAIN REMARK 500 2 DG A 11 0.10 SIDE_CHAIN REMARK 500 2 DG A 14 0.13 SIDE_CHAIN REMARK 500 3 DG A 1 0.11 SIDE_CHAIN REMARK 500 3 DG A 6 0.06 SIDE_CHAIN REMARK 500 3 DG A 11 0.09 SIDE_CHAIN REMARK 500 3 DG A 14 0.14 SIDE_CHAIN REMARK 500 4 DG A 1 0.13 SIDE_CHAIN REMARK 500 4 DG A 11 0.08 SIDE_CHAIN REMARK 500 4 DG A 14 0.13 SIDE_CHAIN REMARK 500 5 DG A 1 0.12 SIDE_CHAIN REMARK 500 5 DG A 6 0.07 SIDE_CHAIN REMARK 500 5 DG A 11 0.06 SIDE_CHAIN REMARK 500 5 DG A 14 0.13 SIDE_CHAIN REMARK 500 6 DG A 1 0.10 SIDE_CHAIN REMARK 500 6 DG A 11 0.09 SIDE_CHAIN REMARK 500 6 DG A 14 0.12 SIDE_CHAIN REMARK 500 7 DG A 1 0.13 SIDE_CHAIN REMARK 500 7 DG A 6 0.07 SIDE_CHAIN REMARK 500 7 DG A 11 0.08 SIDE_CHAIN REMARK 500 7 DG A 14 0.13 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PHOSPHATE GROUP IN T3 IS MISSING DUE TO THE REMARK 999 5'-3' INVERSION OF THIS STRAND. DBREF 2IDN A 1 15 PDB 2IDN 2IDN 1 15 SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 A 15 DG DG LINK P DG A 1 O3' DG A 2 1555 1555 1.64 LINK P DG A 2 O3' DT A 3 1555 1555 1.64 LINK O5' DT A 3 P DT A 4 1555 1555 1.63 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 247 0 0 0 0 0 0 6 0 0 0 2 END