HEADER DNA 13-MAR-19 6R14 TITLE STRUCTURE OF KITEPLATINATED DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: KITEPLATINATED DNA OLIGOMER, CHAIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: KITEPLATINATED DNA OLIGOMER, CHAIN B; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606 KEYWDS KITEPLATIN, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.MARGIOTTA,P.PAPADIA,K.KUBICEK,M.KREJCIKOVA,K.GKIONIS,J.SPONER REVDAT 1 01-APR-20 6R14 0 JRNL AUTH M.KREJCIKOVA,P.PAPADIA,K.GKIONIS,J.PLATS,E.PETRUZZELLA, JRNL AUTH 2 S.SAVINO,J.D.HOESCHELLE,G.NATILE,J.SPONER,K.KUBICEK, JRNL AUTH 3 N.MARGIOTTA JRNL TITL STRUCTURAL CHARACTERIZATION OF KITEPLATINATED DNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOVEL FORCE-FIELD FOR KITEPT REMARK 4 REMARK 4 6R14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1292101267. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 298 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 MM NA- KITEPLATIN, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC ALIPHATIC; 2D 1H REMARK 210 -1H NOESY; 2D DQF-COSY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HO5' DG B 13 OP2 DG B 14 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 7 C6 DG A 7 N1 -0.045 REMARK 500 2 DG A 7 C6 DG A 7 N1 -0.046 REMARK 500 3 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 4 DG A 7 C6 DG A 7 N1 -0.046 REMARK 500 5 DG A 7 C6 DG A 7 N1 -0.046 REMARK 500 6 DG A 7 C6 DG A 7 N1 -0.046 REMARK 500 7 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 8 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 9 DG A 7 C6 DG A 7 N1 -0.044 REMARK 500 10 DG A 7 C6 DG A 7 N1 -0.044 REMARK 500 11 DG A 7 C6 DG A 7 N1 -0.046 REMARK 500 12 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 13 DG A 7 C6 DG A 7 N1 -0.043 REMARK 500 14 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 15 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 16 DG A 7 C6 DG A 7 N1 -0.047 REMARK 500 17 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 18 DG A 7 C6 DG A 7 N1 -0.045 REMARK 500 19 DG A 7 C6 DG A 7 N1 -0.046 REMARK 500 20 DG A 7 C6 DG A 7 N1 -0.045 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. = 2.1 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 7 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DC A 8 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 8 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 10 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC A 12 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG B 13 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 18 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 19 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 20 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 22 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG B 23 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG B 23 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 24 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 874 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 DA A 5 0.07 SIDE CHAIN REMARK 500 1 DC A 11 0.06 SIDE CHAIN REMARK 500 1 DA B 15 0.06 SIDE CHAIN REMARK 500 1 DT B 20 0.11 SIDE CHAIN REMARK 500 1 DG B 21 0.06 SIDE CHAIN REMARK 500 1 DA B 22 0.06 SIDE CHAIN REMARK 500 2 DA A 5 0.06 SIDE CHAIN REMARK 500 2 DG A 6 0.07 SIDE CHAIN REMARK 500 2 DA B 15 0.07 SIDE CHAIN REMARK 500 2 DC B 18 0.06 SIDE CHAIN REMARK 500 2 DG B 23 0.06 SIDE CHAIN REMARK 500 3 DA A 5 0.05 SIDE CHAIN REMARK 500 3 DG A 6 0.07 SIDE CHAIN REMARK 500 3 DG B 14 0.07 SIDE CHAIN REMARK 500 3 DA B 15 0.07 SIDE CHAIN REMARK 500 3 DC B 19 0.06 SIDE CHAIN REMARK 500 3 DT B 20 0.10 SIDE CHAIN REMARK 500 3 DA B 22 0.06 SIDE CHAIN REMARK 500 4 DA A 5 0.11 SIDE CHAIN REMARK 500 4 DG B 14 0.07 SIDE CHAIN REMARK 500 4 DA B 15 0.06 SIDE CHAIN REMARK 500 4 DT B 20 0.11 SIDE CHAIN REMARK 500 5 DA A 5 0.10 SIDE CHAIN REMARK 500 5 DG A 6 0.10 SIDE CHAIN REMARK 500 5 DA B 15 0.09 SIDE CHAIN REMARK 500 5 DG B 16 0.10 SIDE CHAIN REMARK 500 5 DC B 18 0.06 SIDE CHAIN REMARK 500 5 DC B 19 0.09 SIDE CHAIN REMARK 500 5 DT B 20 0.09 SIDE CHAIN REMARK 500 6 DG A 6 0.06 SIDE CHAIN REMARK 500 6 DC A 12 0.08 SIDE CHAIN REMARK 500 6 DG B 14 0.06 SIDE CHAIN REMARK 500 6 DA B 15 0.06 SIDE CHAIN REMARK 500 6 DT B 20 0.10 SIDE CHAIN REMARK 500 7 DC A 2 0.07 SIDE CHAIN REMARK 500 7 DG B 14 0.06 SIDE CHAIN REMARK 500 7 DT B 20 0.11 SIDE CHAIN REMARK 500 7 DA B 22 0.07 SIDE CHAIN REMARK 500 7 DG B 24 0.05 SIDE CHAIN REMARK 500 8 DA A 5 0.06 SIDE CHAIN REMARK 500 8 DG B 14 0.07 SIDE CHAIN REMARK 500 8 DA B 15 0.07 SIDE CHAIN REMARK 500 8 DC B 19 0.06 SIDE CHAIN REMARK 500 8 DT B 20 0.10 SIDE CHAIN REMARK 500 8 DA B 22 0.07 SIDE CHAIN REMARK 500 9 DA A 5 0.07 SIDE CHAIN REMARK 500 9 DG B 14 0.07 SIDE CHAIN REMARK 500 9 DA B 15 0.06 SIDE CHAIN REMARK 500 9 DT B 20 0.11 SIDE CHAIN REMARK 500 9 DA B 22 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 102 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LN8 A 101 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 N7 REMARK 620 2 LN8 A 101 N2 173.6 REMARK 620 3 LN8 A 101 N1 87.3 98.7 REMARK 620 4 DG A 7 N7 87.7 86.2 173.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LN8 A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34378 RELATED DB: BMRB REMARK 900 STRUCTURE OF KITEPLATINATED DSDNA DBREF 6R14 A 1 12 PDB 6R14 6R14 1 12 DBREF 6R14 B 13 24 PDB 6R14 6R14 13 24 SEQRES 1 A 12 DC DC DT DC DA DG DG DC DC DT DC DC SEQRES 1 B 12 DG DG DA DG DG DC DC DT DG DA DG DG HET LN8 A 101 23 HETNAM LN8 KITEPLATIN FORMUL 3 LN8 C6 H14 CL2 N2 PT 2+ LINK N7 DG A 6 PT1 LN8 A 101 1555 1555 2.02 LINK N7 DG A 7 PT1 LN8 A 101 1555 1555 2.01 SITE 1 AC1 7 DA A 5 DG A 6 DG A 7 DC A 8 SITE 2 AC1 7 DG B 16 DG B 17 DC B 18 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