HEADER DNA 22-JAN-11 2L8P TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE POTENT ANTI-POXVIRUS TITLE 2 AGENT CIDOFOVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*GP*(L8P)P*TP*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*AP*GP*CP*AP*TP*GP*CP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA, POXVIRUS, HPMPC EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR O.JULIEN,J.R.BEADLE,W.C.MAGEE,S.CHATTERJEE,K.Y.HOSTETLER,D.H.EVANS, AUTHOR 2 B.D.SYKES REVDAT 2 02-MAR-11 2L8P 1 JRNL REVDAT 1 23-FEB-11 2L8P 0 JRNL AUTH O.JULIEN,J.R.BEADLE,W.C.MAGEE,S.CHATTERJEE,K.Y.HOSTETLER, JRNL AUTH 2 D.H.EVANS,B.D.SYKES JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE POTENT JRNL TITL 2 ANTI-POXVIRUS AGENT CIDOFOVIR. JRNL REF J.AM.CHEM.SOC. V. 133 2264 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21280608 JRNL DOI 10.1021/JA109823E REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE UPPER BOUNDS OBTAINED FROM REMARK 3 MARDIGRAS WERE MULTIPLIED BY A FACTOR 1.25 BEFORE BEING EXPORTED REMARK 3 TO AMBER 10 FOR A 25 PS SIMULATED ANNEALING PROTOCOL. THE REMARK 3 SIMULATED ANNEALING PROTOCOL USING THE PAIRWISE GENERALIZED BORN REMARK 3 MODEL WAS AS FOLLOWS: THE TEMPERATURE OF THE SYSTEM WAS KEPT REMARK 3 CONSTANT AT 600 K DURING THE FIRST 5 PS, COOLED DOWN SLOWLY TO REMARK 3 100 K BETWEEN 5-18 PS, AND COOLED DOWN TO 0 K FOR THE LAST 7 PS. REMARK 3 THE PROTOCOL WAS REPEATED 50 TIMES TO OBTAIN AN NMR ENSEMBLE WITH REMARK 3 THE 10 LOWEST RMSD STRUCTURES. THE STRUCTURE WITH THE LOWEST RMSD REMARK 3 OF THE ENSEMBLE WAS PUT BACK INTO MARDIGRAS FOR A SECOND AND REMARK 3 THIRD CYCLE OF NOE CALIBRATION AND STRUCTURE CALCULATIONS. REMARK 4 REMARK 4 2L8P COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-11. REMARK 100 THE RCSB ID CODE IS RCSB102096. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0-7.2 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM CIDOFOVIR DNA DUPLEX, 95% REMARK 210 H2O/5% 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; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 2.1B, NMRPIPE 4.9, NMRVIEW REMARK 210 8.0.B30, MARDIGRAS, AMBER 10, REMARK 210 CORMA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST RMSD TO AVERAGE STRUCTURE 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 L8P A 7 O6 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 H22 DG A 2 O2 DC B 23 1.79 REMARK 500 H22 DG A 6 O2 DC B 19 1.81 REMARK 500 H22 DG A 11 O2 DC B 14 1.83 REMARK 500 O2 L8P A 7 H22 DG B 18 1.83 REMARK 500 O2 DC A 10 H22 DG B 15 1.83 REMARK 500 O2 DC A 12 H22 DG B 13 1.84 REMARK 500 O2 DC A 1 H22 DG B 24 1.84 REMARK 500 H41 DC A 3 O6 DG B 22 1.86 REMARK 500 O2 DC A 3 H22 DG B 22 1.87 REMARK 500 O4 DT A 5 H61 DA B 20 1.87 REMARK 500 O6 DG A 11 H41 DC B 14 1.88 REMARK 500 H41 DC A 10 O6 DG B 15 1.89 REMARK 500 H3 DT A 8 N1 DA B 17 1.89 REMARK 500 N1 DA A 4 H3 DT B 21 1.89 REMARK 500 HN4 L8P A 7 O6 DG B 18 1.89 REMARK 500 H41 DC A 1 O6 DG B 24 1.89 REMARK 500 H61 DA A 9 O4 DT B 16 1.90 REMARK 500 O4 DT A 8 H61 DA B 17 1.90 REMARK 500 H61 DA A 4 O4 DT B 21 1.90 REMARK 500 O6 DG A 6 H41 DC B 19 1.91 REMARK 500 N1 DA A 9 H3 DT B 16 1.92 REMARK 500 H41 DC A 12 O6 DG B 13 1.92 REMARK 500 H3 DT A 5 N1 DA B 20 1.93 REMARK 500 H1 DG A 11 N3 DC B 14 1.93 REMARK 500 O6 DG A 2 H41 DC B 23 1.93 REMARK 500 H1 DG A 2 N3 DC B 23 1.94 REMARK 500 N3 DC A 3 H1 DG B 22 1.94 REMARK 500 N3 DC A 10 H1 DG B 15 1.94 REMARK 500 H1 DG A 6 N3 DC B 19 1.94 REMARK 500 N3 DC A 1 H1 DG B 24 1.94 REMARK 500 N3 L8P A 7 H1 DG B 18 1.95 REMARK 500 N3 DC A 12 H1 DG B 13 1.96 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 B 13 C5' DG B 13 C4' 0.044 REMARK 500 3 DA B 20 C5' DA B 20 C4' 0.049 REMARK 500 5 DG B 13 C5' DG B 13 C4' 0.042 REMARK 500 8 DG B 13 C5' DG B 13 C4' 0.043 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 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC B 14 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 19 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC B 19 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 19 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA B 20 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA B 20 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 20 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 3 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 383 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 B 21 0.07 SIDE CHAIN REMARK 500 2 DG A 6 0.06 SIDE CHAIN REMARK 500 3 DG A 6 0.07 SIDE CHAIN REMARK 500 3 DT B 21 0.06 SIDE CHAIN REMARK 500 6 DA B 20 0.05 SIDE CHAIN REMARK 500 7 DG A 6 0.06 SIDE CHAIN REMARK 500 7 DT A 8 0.08 SIDE CHAIN REMARK 500 7 DT B 16 0.08 SIDE CHAIN REMARK 500 9 DT B 21 0.07 SIDE CHAIN REMARK 500 10 DT A 8 0.12 SIDE CHAIN REMARK 500 10 DT B 16 0.09 SIDE CHAIN REMARK 500 10 DG B 18 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17422 RELATED DB: BMRB DBREF 2L8P A 1 12 PDB 2L8P 2L8P 1 12 DBREF 2L8P B 13 24 PDB 2L8P 2L8P 13 24 SEQRES 1 A 12 DC DG DC DA DT DG L8P DT DA DC DG DC SEQRES 1 B 12 DG DC DG DT DA DG DC DA DT DG DC DG HET L8P A 7 28 HETNAM L8P ({[(2S)-1-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-3- HETNAM 2 L8P HYDROXYPROPAN-2-YL]OXY}METHYL)PHOSPHONIC ACID HETSYN L8P CIDOFOVIR FORMUL 1 L8P C8 H14 N3 O6 P 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 248 0 1 0 0 0 0 6 0 0 0 2 END