HEADER DNA BINDING PROTEIN/DNA 08-MAR-10 2KV6 TITLE TETRAPEPTIDE KWKK CONJUGATED TO OLIGONUCLEOTIDE DUPLEX BY A TITLE 2 TRIMETHYLENE TETHER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: KWKK TETRAPEPTIDE; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS DNA-PEPTIDE CONJUGATE, TRIMETHYLENE, ACROLEIN-DG ADDUCT, DNA-PEPTIDE KEYWDS 2 COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR H.HUANG,I.D.KOZEKOV,A.KOZEKOVA,C.J.RIZZO,A.MCCULLOUGH,R.S.LLOYD, AUTHOR 2 M.P.STONE REVDAT 3 16-OCT-24 2KV6 1 REMARK LINK REVDAT 2 11-AUG-10 2KV6 1 JRNL REVDAT 1 21-JUL-10 2KV6 0 JRNL AUTH H.HUANG,I.D.KOZEKOV,A.KOZEKOVA,C.J.RIZZO,A.K.MCCULLOUGH, JRNL AUTH 2 R.S.LLOYD,M.P.STONE JRNL TITL MINOR GROOVE ORIENTATION OF THE KWKK PEPTIDE TETHERED VIA JRNL TITL 2 THE N-TERMINAL AMINE TO THE ACROLEIN-DERIVED JRNL TITL 3 1,N(2)-GAMMA-HYDROXYPROPANODEOXYGUANOSINE LESION WITH A JRNL TITL 4 TRIMETHYLENE LINKAGE . JRNL REF BIOCHEMISTRY V. 49 6155 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20604523 JRNL DOI 10.1021/BI100364F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000101612. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.3 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM DNA (5' REMARK 210 -D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')-1, 0.8 MM DNA (5'-D(* REMARK 210 GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3')-2, 0.8 MM ENTITY_3-3, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 24 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2KV6 A 1 12 PDB 2KV6 2KV6 1 12 DBREF 2KV6 B 13 24 PDB 2KV6 2KV6 13 24 DBREF 2KV6 C 26 29 PDB 2KV6 2KV6 26 29 SEQRES 1 A 12 DG DC DT DA DG DC 0AD DA DG DT DC DC SEQRES 1 B 12 DG DG DA DC DT DC DG DC DT DA DG DC SEQRES 1 C 4 LYS TRP LYS LYS MODRES 2KV6 0AD A 7 DG HET 0AD A 7 41 HETNAM 0AD 2'-DEOXY-N-PROPYLGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 0AD C13 H20 N5 O7 P LINK C6A 0AD A 7 N LYS C 26 1555 1555 1.49 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 HETATM 189 P 0AD A 7 -12.307 -1.825 13.905 1.00 0.00 P HETATM 190 OP1 0AD A 7 -12.486 -1.018 15.138 1.00 0.00 O HETATM 191 OP2 0AD A 7 -13.501 -2.460 13.291 1.00 0.00 O HETATM 192 O5' 0AD A 7 -11.224 -2.975 14.212 1.00 0.00 O HETATM 193 C5' 0AD A 7 -10.903 -3.959 13.235 1.00 0.00 C HETATM 194 C4' 0AD A 7 -9.699 -4.823 13.635 1.00 0.00 C HETATM 195 O4' 0AD A 7 -8.511 -4.036 13.608 1.00 0.00 O HETATM 196 C3' 0AD A 7 -9.821 -5.460 15.032 1.00 0.00 C HETATM 197 O3' 0AD A 7 -9.427 -6.824 14.940 1.00 0.00 O HETATM 198 C2' 0AD A 7 -8.836 -4.623 15.847 1.00 0.00 C HETATM 199 C1' 0AD A 7 -7.781 -4.304 14.791 1.00 0.00 C HETATM 200 N9 0AD A 7 -6.896 -3.164 15.127 1.00 0.00 N HETATM 201 C8 0AD A 7 -7.191 -1.977 15.754 1.00 0.00 C HETATM 202 N7 0AD A 7 -6.169 -1.168 15.880 1.00 0.00 N HETATM 203 C5 0AD A 7 -5.108 -1.888 15.313 1.00 0.00 C HETATM 204 C6 0AD A 7 -3.708 -1.583 15.161 1.00 0.00 C HETATM 205 O6 0AD A 7 -3.076 -0.585 15.506 1.00 0.00 O HETATM 206 N1 0AD A 7 -2.986 -2.584 14.545 1.00 0.00 N HETATM 207 C2 0AD A 7 -3.502 -3.785 14.155 1.00 0.00 C HETATM 208 N2 0AD A 7 -2.619 -4.663 13.686 1.00 0.00 N HETATM 209 C4A 0AD A 7 -2.831 -6.075 13.326 1.00 0.00 C HETATM 210 C5A 0AD A 7 -2.412 -6.325 11.874 1.00 0.00 C HETATM 211 N3 0AD A 7 -4.798 -4.103 14.291 1.00 0.00 N HETATM 212 C4 0AD A 7 -5.548 -3.114 14.864 1.00 0.00 C HETATM 213 C6A 0AD A 7 -2.352 -7.821 11.536 1.00 0.00 C HETATM 214 H5'1 0AD A 7 -10.673 -3.471 12.287 1.00 0.00 H HETATM 215 H5'2 0AD A 7 -11.765 -4.610 13.082 1.00 0.00 H HETATM 216 H4' 0AD A 7 -9.604 -5.623 12.898 1.00 0.00 H HETATM 217 H3' 0AD A 7 -10.838 -5.371 15.422 1.00 0.00 H HETATM 218 H1' 0AD A 7 -7.168 -5.198 14.638 1.00 0.00 H HETATM 219 H2'1 0AD A 7 -9.331 -3.717 16.197 1.00 0.00 H HETATM 220 H2'2 0AD A 7 -8.408 -5.173 16.683 1.00 0.00 H HETATM 221 H8 0AD A 7 -8.190 -1.730 16.095 1.00 0.00 H HETATM 222 H1 0AD A 7 -1.989 -2.439 14.469 1.00 0.00 H HETATM 223 H2 0AD A 7 -1.652 -4.359 13.665 1.00 0.00 H HETATM 224 H4A1 0AD A 7 -3.871 -6.379 13.466 1.00 0.00 H HETATM 225 H4A2 0AD A 7 -2.203 -6.683 13.977 1.00 0.00 H HETATM 226 H5A1 0AD A 7 -3.144 -5.843 11.224 1.00 0.00 H HETATM 227 H5A2 0AD A 7 -1.427 -5.883 11.702 1.00 0.00 H HETATM 228 H17 0AD A 7 -1.583 -8.293 12.157 1.00 0.00 H HETATM 229 H19 0AD A 7 -3.326 -8.270 11.763 1.00 0.00 H TER 388 DC A 12 TER 768 DC B 24 TER 861 LYS C 29 CONECT 189 190 191 192 CONECT 190 189 CONECT 191 189 CONECT 192 189 193 CONECT 193 192 194 214 215 CONECT 194 193 195 196 216 CONECT 195 194 199 CONECT 196 194 197 198 217 CONECT 197 196 CONECT 198 196 199 219 220 CONECT 199 195 198 200 218 CONECT 200 199 201 212 CONECT 201 200 202 221 CONECT 202 201 203 CONECT 203 202 204 212 CONECT 204 203 205 206 CONECT 205 204 CONECT 206 204 207 222 CONECT 207 206 208 211 CONECT 208 207 209 223 CONECT 209 208 210 224 225 CONECT 210 209 213 226 227 CONECT 211 207 212 CONECT 212 200 203 211 CONECT 213 210 228 229 769 CONECT 214 193 CONECT 215 193 CONECT 216 194 CONECT 217 196 CONECT 218 199 CONECT 219 198 CONECT 220 198 CONECT 221 201 CONECT 222 206 CONECT 223 208 CONECT 224 209 CONECT 225 209 CONECT 226 210 CONECT 227 210 CONECT 228 213 CONECT 229 213 CONECT 769 213 MASTER 118 0 1 0 0 0 0 6 531 3 42 3 END