HEADER DNA 22-JAN-24 8Y0F TITLE SOLUTION NMR STRUCTURE OF THE PTK7-BINDING DNA APTAMER SGC8C COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA; 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 DNA APTAMER, PROTEIN TYROSINE KINASE 7, THREE-WAY JUNCTION, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.HE,L.WAN,P.GUO,D.HAN REVDAT 2 24-JUL-24 8Y0F 1 JRNL REVDAT 1 26-JUN-24 8Y0F 0 JRNL AUTH A.HE,L.WAN,Y.ZHANG,Z.YAN,P.GUO,D.HAN,W.TAN JRNL TITL STRUCTURE-BASED INVESTIGATION OF A DNA APTAMER TARGETING JRNL TITL 2 PTK7 REVEALS AN INTRICATE 3D FOLD GUIDING FUNCTIONAL JRNL TITL 3 OPTIMIZATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 60121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38985770 JRNL DOI 10.1073/PNAS.2404060121 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS, AMBER REMARK 3 AUTHORS : ABRAHAM, ALEKSEENKO, BAUER, BERGH, BLAU, BRIAND, REMARK 3 DOIJADE,... AND ZHMUROV (GROMACS), 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 8Y0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043537. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 15 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 0.5 MM DNA, 0.02 MM DSS, 10 MM REMARK 210 SODIUM PHOSPHATE, 5 MM MAGNESIUM REMARK 210 CHLORIDE, 99.96%D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY 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 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 7 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 18 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA A 24 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 25 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 29 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT A 30 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DT A 32 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA A 33 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DA A 33 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 34 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 37 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 38 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 39 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 40 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 41 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 7 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DG A 12 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DC A 13 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 16 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DC A 19 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 21 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DG A 22 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DA A 23 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 348 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 DC A 3 0.11 SIDE CHAIN REMARK 500 1 DT A 4 0.08 SIDE CHAIN REMARK 500 1 DT A 8 0.07 SIDE CHAIN REMARK 500 1 DG A 9 0.10 SIDE CHAIN REMARK 500 1 DC A 10 0.08 SIDE CHAIN REMARK 500 1 DG A 12 0.15 SIDE CHAIN REMARK 500 1 DC A 15 0.07 SIDE CHAIN REMARK 500 1 DC A 18 0.12 SIDE CHAIN REMARK 500 1 DT A 30 0.16 SIDE CHAIN REMARK 500 1 DG A 31 0.09 SIDE CHAIN REMARK 500 1 DG A 35 0.07 SIDE CHAIN REMARK 500 1 DT A 38 0.08 SIDE CHAIN REMARK 500 2 DC A 3 0.10 SIDE CHAIN REMARK 500 2 DT A 4 0.12 SIDE CHAIN REMARK 500 2 DA A 6 0.06 SIDE CHAIN REMARK 500 2 DC A 7 0.07 SIDE CHAIN REMARK 500 2 DG A 9 0.07 SIDE CHAIN REMARK 500 2 DC A 10 0.14 SIDE CHAIN REMARK 500 2 DT A 11 0.07 SIDE CHAIN REMARK 500 2 DG A 14 0.09 SIDE CHAIN REMARK 500 2 DC A 18 0.11 SIDE CHAIN REMARK 500 2 DG A 20 0.10 SIDE CHAIN REMARK 500 2 DA A 24 0.06 SIDE CHAIN REMARK 500 2 DC A 29 0.09 SIDE CHAIN REMARK 500 2 DG A 31 0.09 SIDE CHAIN REMARK 500 2 DG A 35 0.10 SIDE CHAIN REMARK 500 2 DT A 37 0.10 SIDE CHAIN REMARK 500 3 DC A 3 0.10 SIDE CHAIN REMARK 500 3 DT A 4 0.09 SIDE CHAIN REMARK 500 3 DA A 6 0.06 SIDE CHAIN REMARK 500 3 DC A 7 0.17 SIDE CHAIN REMARK 500 3 DG A 9 0.12 SIDE CHAIN REMARK 500 3 DC A 10 0.10 SIDE CHAIN REMARK 500 3 DG A 14 0.14 SIDE CHAIN REMARK 500 3 DG A 31 0.08 SIDE CHAIN REMARK 500 3 DT A 32 0.06 SIDE CHAIN REMARK 500 3 DG A 35 0.08 SIDE CHAIN REMARK 500 3 DG A 36 0.07 SIDE CHAIN REMARK 500 3 DT A 38 0.13 SIDE CHAIN REMARK 500 4 DC A 3 0.08 SIDE CHAIN REMARK 500 4 DT A 4 0.10 SIDE CHAIN REMARK 500 4 DG A 9 0.08 SIDE CHAIN REMARK 500 4 DC A 10 0.08 SIDE CHAIN REMARK 500 4 DG A 17 0.07 SIDE CHAIN REMARK 500 4 DC A 18 0.15 SIDE CHAIN REMARK 500 4 DG A 21 0.07 SIDE CHAIN REMARK 500 4 DG A 31 0.08 SIDE CHAIN REMARK 500 4 DT A 32 0.13 SIDE CHAIN REMARK 500 4 DG A 35 0.07 SIDE CHAIN REMARK 500 4 DG A 36 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 128 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36640 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF THE PTK7-BINDING DNA APTAMER SGC8C DBREF 8Y0F A 1 41 PDB 8Y0F 8Y0F 1 41 SEQRES 1 A 41 DA DT DC DT DA DA DC DT DG DC DT DG DC SEQRES 2 A 41 DG DC DC DG DC DC DG DG DG DA DA DA DA SEQRES 3 A 41 DT DA DC DT DG DT DA DC DG DG DT DT DA SEQRES 4 A 41 DG DA 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