HEADER DNA 13-FEB-13 2M53 TITLE G-RICH VEGF APTAMER WITH LNA MODIFICATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-RICH VEGF APTAMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS APTAMER, DNA, G-QUADRUPLEX, LOCKED NUCLEIC ACID, VEGF EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.MARUSIC,R.N.VEEDU,J.PLAVEC REVDAT 3 24-AUG-22 2M53 1 JRNL REVDAT 2 19-JUN-19 2M53 1 SOURCE REMARK LINK REVDAT 1 28-AUG-13 2M53 0 JRNL AUTH M.MARUSIC,R.N.VEEDU,J.WENGEL,J.PLAVEC JRNL TITL G-RICH VEGF APTAMER WITH LOCKED AND UNLOCKED NUCLEIC ACID JRNL TITL 2 MODIFICATIONS EXHIBITS A UNIQUE G-QUADRUPLEX FOLD. JRNL REF NUCLEIC ACIDS RES. V. 41 9524 2013 JRNL REFN ESSN 1362-4962 JRNL PMID 23935071 JRNL DOI 10.1093/NAR/GKT697 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 11, AMBER 11 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, ... REMARK 3 AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 298; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100; 100; 50 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM DNA(25-MER)-1, 10 MM REMARK 210 POTASSIUM PHOSPHATE-2, 90 MM REMARK 210 POTASSIUM CHLORIDE-3, 90% H2O/10% REMARK 210 D2O; 0.5 MM DNA(25-MER)-4, 10 REMARK 210 MM POTASSIUM PHOSPHATE-5, 40 MM REMARK 210 POTASSIUM CHLORIDE-6, 90% H2O/10% REMARK 210 D2O; 0.5 MM DNA(25-MER)-7, 10 REMARK 210 MM POTASSIUM PHOSPHATE-8, 90 MM REMARK 210 POTASSIUM CHLORIDE-9, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 11, NMRPIPE, SPARKY, VNMRJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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 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 3 DG A 7 C5' DG A 7 C4' 0.042 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 3 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 6 N3 - C2 - N2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 13 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DC A 17 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 17 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 18 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 22 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT A 22 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 22 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 23 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 23 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 23 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 23 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DA A 25 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 25 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 25 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT A 3 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DG A 6 N3 - C2 - N2 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA A 12 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 354 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 3 0.09 SIDE CHAIN REMARK 500 1 DG A 7 0.16 SIDE CHAIN REMARK 500 1 DG A 10 0.07 SIDE CHAIN REMARK 500 1 DG A 14 0.08 SIDE CHAIN REMARK 500 1 DG A 19 0.07 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DT A 3 0.11 SIDE CHAIN REMARK 500 2 DG A 6 0.06 SIDE CHAIN REMARK 500 2 DG A 7 0.09 SIDE CHAIN REMARK 500 2 DT A 9 0.09 SIDE CHAIN REMARK 500 2 DG A 10 0.07 SIDE CHAIN REMARK 500 2 DG A 11 0.07 SIDE CHAIN REMARK 500 2 DG A 14 0.10 SIDE CHAIN REMARK 500 2 DG A 15 0.06 SIDE CHAIN REMARK 500 2 DG A 16 0.06 SIDE CHAIN REMARK 500 2 DG A 19 0.09 SIDE CHAIN REMARK 500 2 DG A 20 0.06 SIDE CHAIN REMARK 500 2 DT A 22 0.09 SIDE CHAIN REMARK 500 2 DA A 25 0.05 SIDE CHAIN REMARK 500 3 DT A 3 0.07 SIDE CHAIN REMARK 500 3 DG A 7 0.16 SIDE CHAIN REMARK 500 3 DG A 8 0.06 SIDE CHAIN REMARK 500 3 DT A 9 0.11 SIDE CHAIN REMARK 500 3 DG A 10 0.06 SIDE CHAIN REMARK 500 3 DG A 11 0.05 SIDE CHAIN REMARK 500 3 DC A 13 0.06 SIDE CHAIN REMARK 500 3 DG A 14 0.10 SIDE CHAIN REMARK 500 3 DG A 19 0.07 SIDE CHAIN REMARK 500 4 DG A 6 0.07 SIDE CHAIN REMARK 500 4 DG A 7 0.15 SIDE CHAIN REMARK 500 4 DT A 9 0.14 SIDE CHAIN REMARK 500 4 DG A 14 0.10 SIDE CHAIN REMARK 500 4 DG A 19 0.07 SIDE CHAIN REMARK 500 4 DG A 20 0.06 SIDE CHAIN REMARK 500 5 DG A 2 0.06 SIDE CHAIN REMARK 500 5 DT A 3 0.08 SIDE CHAIN REMARK 500 5 DG A 6 0.09 SIDE CHAIN REMARK 500 5 DG A 8 0.08 SIDE CHAIN REMARK 500 5 DT A 9 0.11 SIDE CHAIN REMARK 500 5 DG A 10 0.06 SIDE CHAIN REMARK 500 5 DG A 11 0.07 SIDE CHAIN REMARK 500 5 DG A 14 0.08 SIDE CHAIN REMARK 500 5 DG A 19 0.06 SIDE CHAIN REMARK 500 5 DT A 22 0.06 SIDE CHAIN REMARK 500 6 DT A 3 0.09 SIDE CHAIN REMARK 500 6 DG A 6 0.08 SIDE CHAIN REMARK 500 6 DG A 7 0.12 SIDE CHAIN REMARK 500 6 DG A 8 0.11 SIDE CHAIN REMARK 500 6 DT A 9 0.11 SIDE CHAIN REMARK 500 6 DG A 10 0.05 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 81 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19035 RELATED DB: BMRB DBREF 2M53 A 1 25 PDB 2M53 2M53 1 25 SEQRES 1 A 25 DT DG DT DG LCG DG DG DG DT DG DG DA DC SEQRES 2 A 25 DG DG DG DC DC DG DG LCG DT DA LCG DA MODRES 2M53 LCG A 5 DG MODRES 2M53 LCG A 21 DG MODRES 2M53 LCG A 24 DG HET LCG A 5 35 HET LCG A 21 35 HET LCG A 24 35 HETNAM LCG [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5- HETNAM 2 LCG DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCG PHOSPHATE FORMUL 1 LCG 3(C11 H14 N5 O8 P) LINK O3' DG A 4 P LCG A 5 1555 1555 1.64 LINK O3' LCG A 5 P DG A 6 1555 1555 1.61 LINK O3' DG A 20 P LCG A 21 1555 1555 1.62 LINK O3' LCG A 21 P DT A 22 1555 1555 1.60 LINK O3' DA A 23 P LCG A 24 1555 1555 1.62 LINK O3' LCG A 24 P DA A 25 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