HEADER DNA 28-FEB-18 5ZEV TITLE SOLUTION STRUCTURE OF G-QUADRUPLEX FORMED IN VEGFR-2 PROXIMAL PROMOTER TITLE 2 SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP* COMPND 4 GP*T)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX VEGFR-2 DNA, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.LIU,W.X.LAN REVDAT 4 14-JUN-23 5ZEV 1 REMARK REVDAT 3 20-JUN-18 5ZEV 1 JRNL REVDAT 2 30-MAY-18 5ZEV 1 JRNL REVDAT 1 18-APR-18 5ZEV 0 JRNL AUTH Y.LIU,W.LAN,C.WANG,C.CAO JRNL TITL A PUTATIVE G-QUADRUPLEX STRUCTURE IN THE PROXIMAL PROMOTER JRNL TITL 2 OFVEGFR-2HAS IMPLICATIONS FOR DRUG DESIGN TO INHIBIT TUMOR JRNL TITL 3 ANGIOGENESIS. JRNL REF J. BIOL. CHEM. V. 293 8947 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29666187 JRNL DOI 10.1074/JBC.RA118.002666 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A.T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ZEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006146. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP* REMARK 210 GP*GP*GP*T)-3'), 20 MM POTASSIUM PHOSPHATE, 80 MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 1.0 MM DNA (5'-D(*GP*GP*GP*TP*AP*CP* REMARK 210 CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP*GP*T)-3'), 80 MM REMARK 210 POTASSIUM CHLORIDE, 20 MM POTASSIUM PHOSPHATE, 100% D2O; 0.1 MM REMARK 210 [U-13C; U-15N]-GUA DNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP* REMARK 210 TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP*GP*T)-3'), 80 MM POTASSIUM REMARK 210 CHLORIDE, 20 MM POTASSIUM PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 15 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 4 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 5 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 6 DG A 15 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 7 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 7 DT A 24 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 9 DG A 15 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 10 DG A 15 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 11 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 11 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.5 DEGREES REMARK 500 12 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 13 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 14 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 15 DG A 15 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 16 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 17 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 18 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 19 DG A 15 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 20 DG A 15 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36168 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF G-QUADRUPLEX FORMED IN VEGFR-2 PROXIMAL REMARK 900 PROMOTER SEQUENCE DBREF 5ZEV A 1 24 PDB 5ZEV 5ZEV 1 24 SEQRES 1 A 24 DG DG DG DT DA DC DC DC DG DG DG DT DG SEQRES 2 A 24 DA DG DG DT DG DC DG DG DG DG DT 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