HEADER RNA 30-JUN-25 9PDG TITLE THREE-DIMENSIONAL STRUCTURE OF KINASE INHIBITOR PALBOCICLIB-HIV TAR TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PALBOCICLIB, COMPLEX, HIV-1 TAR, RNA, SMALL MOLECULE-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.R.RAMIREDDY,V.N.VIDADALA,B.CHAUBEY,G.OLSEN,G.VARANI REVDAT 1 04-FEB-26 9PDG 0 JRNL AUTH R.R.RAMIREDDY,V.N.VIDADALA,B.CHAUBEY,G.OLSEN,G.VARANI JRNL TITL THREE-DIMENSIONAL STRUCTURE OF KINASE INHIBITOR JRNL TITL 2 PALBOCICLIB-HIV TAR COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: VERSION 3.8 REMARK 4 REMARK 4 9PDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000296667. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 310; 310; 310; 310; 310; REMARK 210 310; 310; 310; 278; 278; 278; REMARK 210 278; 278; 278 REMARK 210 PH : 5.8; 5.8; 5.0; 5.0; 5.0; 5.0; REMARK 210 5.0; 5.0; 5.0; 5.8; 5.8; 5.8; REMARK 210 5.8; 5.8; 5.8 REMARK 210 IONIC STRENGTH : 20 MM BIS TRIS D19, 50 MM SODIUM REMARK 210 CHLORIDE; 20 MM BIS TRIS D19, 50 REMARK 210 MM SODIUM CHLORIDE; 20 MM SODIUM REMARK 210 ACETATE; 20 MM SODIUM ACETATE; REMARK 210 20 MM SODIUM ACETATE; 20 MM REMARK 210 SODIUM ACETATE; 20 MM SODIUM REMARK 210 ACETATE; 20 MM SODIUM ACETATE; REMARK 210 20 MM SODIUM ACETATE; 20 MM BIS REMARK 210 TRIS D19, 50 MM SODIUM CHLORIDE; REMARK 210 20 MM BIS TRIS D19, 50 MM SODIUM REMARK 210 CHLORIDE; 20 MM BIS TRIS D19, 50 REMARK 210 MM SODIUM CHLORIDE; 20 MM BIS REMARK 210 TRIS D19, 50 MM SODIUM CHLORIDE; REMARK 210 20 MM BIS TRIS D19, 50 MM SODIUM REMARK 210 CHLORIDE; 20 MM BIS TRIS D19, 50 REMARK 210 MM SODIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM; 1 REMARK 210 ATM; 1 ATM; 1 ATM; 1 ATM; 1 ATM; REMARK 210 1 ATM; 1 ATM; 1 ATM; 1 ATM; 1 REMARK 210 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM HIV TAR RNA (29-MER), 90% REMARK 210 H2O/10% D2O; 0.9 NM HIV TAR RNA REMARK 210 (29-MER), 100% D2O; 0.9 NM HIV REMARK 210 TAR RNA (29-MER), 100% D2O; 0.9 REMARK 210 NM [U-99% 13C; U-99% 15N] HIV REMARK 210 TAR RNA (29-MER), 100% D2O; 0.9 REMARK 210 MM [U-99% 13C; U-99% 15N] HIV REMARK 210 TAR RNA (29-MER), 95% H2O/5% D2O; REMARK 210 0.5 MM [U-13C; U-15N]-ADE HIV REMARK 210 TAR RNA (29-MER), 100% D2O; 0.45 REMARK 210 MM [U-13C; U-15N]-ADE HIV TAR REMARK 210 RNA (29-MER), 95% H2O/5% D2O; REMARK 210 0.77 MM [U-13C; U-15N]-ADE, CYT REMARK 210 HIV TAR RNA (29-MER), 100% D2O; REMARK 210 0.75 MM [U-13C; U-15N]-ADE, CYT REMARK 210 HIV TAR RNA (29-MER), 95% H2O/5% REMARK 210 D2O; 0.75 MM [U-13C; U-15N]-GUA, REMARK 210 URA HIV TAR RNA (29-MER), 100% REMARK 210 D2O; 0.7 MM [U-13C; U-15N]-GUA, REMARK 210 URA HIV TAR RNA (29-MER), 95% REMARK 210 H2O/5% D2O; 0.9 MM [U-99% 2H] REMARK 210 HIV TAR RNA (29-MER), 100% D2O; REMARK 210 0.9 MM [U-99% 2H] HIV TAR RNA REMARK 210 (29-MER), 100% D2O; 0.25 MM [U- REMARK 210 99% 2H] HIV TAR RNA (29-MER), REMARK 210 100% D2O; 0.25 MM [U-99% 2H] HIV REMARK 210 TAR RNA (29-MER), 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HMQC; 2D 1H-13C CT- REMARK 210 HSQC ALIPHATIC; 2D 1H-13C CT- REMARK 210 HSQC AROMATIC; 2D FILTERED/ REMARK 210 EDITED NOESY; 3D 1H-13C NOESY; REMARK 210 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 NH2 ONLY; 2D 1H-1N HNNCOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, X-PLOR NIH, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31259 RELATED DB: BMRB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF KINASE INHIBITOR PALBOCICLIB-HIV TAR REMARK 900 COMPLEX DBREF 9PDG A 17 45 PDB 9PDG 9PDG 17 45 SEQRES 1 A 29 G G C A G AP7 U CH U G A G C SEQRES 2 A 29 C U G G G A G C U C U C U SEQRES 3 A 29 G C C MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE MODRES 9PDG CH A 24 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HET AP7 A 22 34 HET CH A 24 32 HET LQQ A 101 62 HETNAM AP7 N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HETNAM LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1- HETNAM 2 LQQ YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE HETSYN LQQ PALBOCICLIB FORMUL 1 AP7 C10 H15 N5 O7 P 1+ FORMUL 1 CH C9 H15 N3 O8 P 1+ FORMUL 2 LQQ C24 H29 N7 O2 LINK O3' G A 21 P AP7 A 22 1555 1555 1.62 LINK O3' AP7 A 22 P U A 23 1555 1555 1.61 LINK O3' U A 23 P CH A 24 1555 1555 1.61 LINK O3' CH A 24 P U A 25 1555 1555 1.61 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 139 186 CONECT 165 175 176 181 187 CONECT 166 167 171 188 CONECT 167 166 168 189 CONECT 168 167 169 CONECT 169 168 170 175 CONECT 170 169 171 173 CONECT 171 166 170 172 CONECT 172 171 190 191 CONECT 173 170 174 CONECT 174 173 175 192 CONECT 175 165 169 174 CONECT 176 165 177 178 193 CONECT 177 176 194 CONECT 178 176 179 180 195 CONECT 179 178 199 CONECT 180 178 181 182 196 CONECT 181 165 180 CONECT 182 180 183 197 198 CONECT 183 182 186 CONECT 184 186 CONECT 185 186 CONECT 186 139 183 184 185 CONECT 187 165 CONECT 188 166 CONECT 189 167 CONECT 190 172 CONECT 191 172 CONECT 192 174 CONECT 193 176 CONECT 194 177 CONECT 195 178 CONECT 196 180 CONECT 197 182 CONECT 198 182 CONECT 199 179 CONECT 207 229 CONECT 229 207 230 231 232 CONECT 230 229 CONECT 231 229 CONECT 232 229 233 CONECT 233 232 234 249 250 CONECT 234 233 235 236 251 CONECT 235 234 240 CONECT 236 234 237 238 252 CONECT 237 236 261 CONECT 238 236 239 240 253 CONECT 239 238 254 CONECT 240 235 238 241 255 CONECT 241 240 242 248 CONECT 242 241 243 244 CONECT 243 242 CONECT 244 242 245 256 CONECT 245 244 246 247 CONECT 246 245 257 258 CONECT 247 245 248 259 CONECT 248 241 247 260 CONECT 249 233 CONECT 250 233 CONECT 251 234 CONECT 252 236 CONECT 253 238 CONECT 254 239 CONECT 255 240 CONECT 256 244 CONECT 257 246 CONECT 258 246 CONECT 259 247 CONECT 260 248 CONECT 261 237 CONECT 934 935 CONECT 935 934 936 937 CONECT 936 935 967 968 969 CONECT 937 935 938 952 CONECT 938 937 939 940 CONECT 939 938 970 971 972 CONECT 940 938 941 945 CONECT 941 940 942 973 CONECT 942 941 943 CONECT 943 942 944 954 CONECT 944 943 945 CONECT 945 940 944 946 CONECT 946 945 947 952 CONECT 947 946 948 951 974 CONECT 948 947 949 975 976 CONECT 949 948 950 977 978 CONECT 950 949 951 979 980 CONECT 951 947 950 981 982 CONECT 952 937 946 953 CONECT 953 952 CONECT 954 943 955 983 CONECT 955 954 956 960 CONECT 956 955 957 CONECT 957 956 958 984 CONECT 958 957 959 961 CONECT 959 958 960 985 CONECT 960 955 959 986 CONECT 961 958 962 966 CONECT 962 961 963 987 988 CONECT 963 962 964 989 990 CONECT 964 963 965 991 CONECT 965 964 966 992 993 CONECT 966 961 965 994 995 CONECT 967 936 CONECT 968 936 CONECT 969 936 CONECT 970 939 CONECT 971 939 CONECT 972 939 CONECT 973 941 CONECT 974 947 CONECT 975 948 CONECT 976 948 CONECT 977 949 CONECT 978 949 CONECT 979 950 CONECT 980 950 CONECT 981 951 CONECT 982 951 CONECT 983 954 CONECT 984 957 CONECT 985 959 CONECT 986 960 CONECT 987 962 CONECT 988 962 CONECT 989 963 CONECT 990 963 CONECT 991 964 CONECT 992 965 CONECT 993 965 CONECT 994 966 CONECT 995 966 MASTER 125 0 3 0 0 0 0 6 648 1 132 3 END