HEADER DNA 02-JAN-20 6LNZ TITLE NMR SOLUTION STRUCTURE OF VEGF G-QUADRUPLEX BOUND A NON-PLANAR TITLE 2 CYCLOMETALATED-CARBENE PLATINUM(II) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*GP*GP*GP*GP*CP*GP*GP*GP*CP*CP*TP*TP*GP*GP*GP*CP*GP*GP*GP*GP*T)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 SYNONYM: VEGF G-QUADRUPLEX DNA; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS VEGF G-QUADRUPLEX, SOLUTION STRUCTURE, DNA-LIGAND COMPLEX, PLATINUM KEYWDS 2 COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR W.LIU,B.Z.ZHU,Z.W.MAO REVDAT 3 01-MAY-24 6LNZ 1 REMARK REVDAT 2 04-AUG-21 6LNZ 1 JRNL REVDAT 1 13-JAN-21 6LNZ 0 JRNL AUTH B.C.ZHU,J.HE,W.LIU,X.Y.XIA,L.Y.LIU,B.B.LIANG,H.G.YAO,B.LIU, JRNL AUTH 2 L.N.JI,Z.W.MAO JRNL TITL SELECTIVITY AND TARGETING OF G-QUADRUPLEX BINDERS ACTIVATED JRNL TITL 2 BY ADAPTIVE BINDING AND CONTROLLED BY CHEMICAL KINETICS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 15340 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 33899272 JRNL DOI 10.1002/ANIE.202104624 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, DISCOVERY STUDIO REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), BIOVIA (DISCOVERY STUDIO) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300014945. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM VEGF G-QUADRUPLEX DNA, REMARK 210 1.0 MM LLPTCL, 75 MM POTASSIUM REMARK 210 CHLORIDE, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: 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 DC A 11 C5' DC A 11 C4' 0.077 REMARK 500 1 DC A 11 C4' DC A 11 C3' 0.081 REMARK 500 1 DT A 12 C5' DT A 12 C4' 0.127 REMARK 500 1 DT A 12 C4' DT A 12 C3' 0.126 REMARK 500 1 DT A 12 C5 DT A 12 C7 0.052 REMARK 500 1 DT A 13 C5 DT A 13 C7 0.052 REMARK 500 1 DG A 14 O3' DG A 15 P 0.084 REMARK 500 1 DG A 15 P DG A 15 OP1 0.107 REMARK 500 1 DG A 15 P DG A 15 OP2 0.104 REMARK 500 1 DT A 22 C5 DT A 22 C7 0.053 REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.055 REMARK 500 2 DG A 9 O3' DC A 10 P -0.078 REMARK 500 2 DC A 11 C5' DC A 11 C4' 0.075 REMARK 500 2 DT A 12 C5' DT A 12 C4' 0.059 REMARK 500 2 DT A 12 C5 DT A 12 C7 0.052 REMARK 500 2 DT A 13 P DT A 13 OP2 0.120 REMARK 500 2 DT A 13 C5 DT A 13 C7 0.051 REMARK 500 2 DG A 14 P DG A 14 OP2 0.110 REMARK 500 2 DG A 14 C5' DG A 14 C4' 0.083 REMARK 500 2 DG A 15 C5' DG A 15 C4' 0.046 REMARK 500 2 DG A 21 C5' DG A 21 C4' 0.059 REMARK 500 2 DT A 22 C5 DT A 22 C7 0.052 REMARK 500 3 DT A 12 C5' DT A 12 C4' 0.106 REMARK 500 3 DT A 12 C4' DT A 12 C3' 0.064 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.052 REMARK 500 3 DT A 13 C5' DT A 13 C4' 0.053 REMARK 500 3 DT A 13 C5 DT A 13 C7 0.052 REMARK 500 3 DG A 15 C5' DG A 15 C4' 0.055 REMARK 500 3 DG A 21 C5' DG A 21 C4' 0.057 REMARK 500 3 DT A 22 P DT A 22 O5' -0.063 REMARK 500 3 DT A 22 C5 DT A 22 C7 0.053 REMARK 500 4 DG A 2 C5' DG A 2 C4' 0.056 REMARK 500 4 DG A 9 C5' DG A 9 C4' 0.046 REMARK 500 4 DC A 10 C5' DC A 10 C4' 0.055 REMARK 500 4 DC A 11 C5' DC A 11 C4' 0.095 REMARK 500 4 DT A 12 C5' DT A 12 C4' 0.079 REMARK 500 4 DT A 12 C5 DT A 12 C7 0.052 REMARK 500 4 DT A 12 O3' DT A 13 P -0.125 REMARK 500 4 DT A 13 C5 DT A 13 C7 0.052 REMARK 500 4 DG A 14 P DG A 14 OP1 0.104 REMARK 500 4 DG A 21 C5' DG A 21 C4' 0.048 REMARK 500 4 DT A 22 C5 DT A 22 C7 0.052 REMARK 500 5 DG A 5 C5' DG A 5 C4' 0.057 REMARK 500 5 DC A 6 P DC A 6 O5' -0.061 REMARK 500 5 DC A 6 O3' DG A 7 P 0.121 REMARK 500 5 DG A 9 O3' DC A 10 P -0.075 REMARK 500 5 DT A 12 C5' DT A 12 C4' 0.113 REMARK 500 5 DT A 12 C3' DT A 12 C2' 0.091 REMARK 500 5 DT A 12 C2' DT A 12 C1' 0.082 REMARK 500 5 DT A 12 O3' DT A 12 C3' 0.084 REMARK 500 REMARK 500 THIS ENTRY HAS 184 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 9 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC A 10 O3' - P - O5' ANGL. DEV. = 12.4 DEGREES REMARK 500 1 DC A 10 O3' - P - OP1 ANGL. DEV. = 11.4 DEGREES REMARK 500 1 DC A 10 OP1 - P - OP2 ANGL. DEV. = -17.5 DEGREES REMARK 500 1 DC A 10 O5' - P - OP2 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DC A 10 N1 - C1' - C2' ANGL. DEV. = 9.4 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DC A 11 O3' - P - O5' ANGL. DEV. = 13.2 DEGREES REMARK 500 1 DC A 11 OP1 - P - OP2 ANGL. DEV. = -11.7 DEGREES REMARK 500 1 DC A 11 C5' - C4' - O4' ANGL. DEV. = -12.3 DEGREES REMARK 500 1 DC A 11 C4' - C3' - O3' ANGL. DEV. = 13.4 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 11 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DT A 12 O3' - P - O5' ANGL. DEV. = 23.1 DEGREES REMARK 500 1 DT A 12 O5' - P - OP2 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 12 P - O5' - C5' ANGL. DEV. = -11.4 DEGREES REMARK 500 1 DT A 12 C4' - C3' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 14 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 14 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DG A 15 O3' - P - O5' ANGL. DEV. = 13.3 DEGREES REMARK 500 1 DG A 15 O3' - P - OP1 ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DG A 15 OP1 - P - OP2 ANGL. DEV. = -17.8 DEGREES REMARK 500 1 DG A 15 O5' - P - OP2 ANGL. DEV. = -7.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1211 ANGLE 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 EL9 A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36308 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF VEGF G-QUADRUPLEX BOUND A NON-PLANAR REMARK 900 CYCLOMETALATED-CARBENE PLATINUM(II) COMPLEX DBREF 6LNZ A 1 22 PDB 6LNZ 6LNZ 1 22 SEQRES 1 A 22 DC DG DG DG DG DC DG DG DG DC DC DT DT SEQRES 2 A 22 DG DG DG DC DG DG DG DG DT HET EL9 A 101 42 HETNAM EL9 CYCLOMETALATED-CARBENE PLATINUM(II) COMPLEX FORMUL 2 EL9 C20 H15 F2 N4 PT SITE 1 AC1 5 DG A 9 DC A 10 DG A 16 DG A 20 SITE 2 AC1 5 DG A 21 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