HEADER HYDROLASE/HYDROLASE INHIBITOR 29-FEB-08 2K1C OBSLTE 29-DEC-10 2K1C 2L6E TITLE NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF HIV-1 CAPSID IN COMPLEX WITH TITLE 2 PEPTIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN P24; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 280-363; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NYAD-13 PEPTIDE INHIBITOR; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG-POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET14B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS ALPHA-HELIX, HYDROCARBON STAPLING, AIDS, ASPARTYL PROTEASE, CAPSID KEYWDS 2 MATURATION, CAPSID PROTEIN, DNA INTEGRATION, DNA RECOMBINATION, DNA- KEYWDS 3 DIRECTED DNA POLYMERASE, ENDONUCLEASE, LIPOPROTEIN, MAGNESIUM, KEYWDS 4 MEMBRANE, METAL-BINDING, MULTIFUNCTIONAL ENZYME, MYRISTATE, KEYWDS 5 NUCLEASE, NUCLEOTIDYLTRANSFERASE, NUCLEUS, PHOSPHOPROTEIN, PROTEASE, KEYWDS 6 RNA-BINDING, RNA-DIRECTED DNA POLYMERASE, TRANSFERASE, VIRAL KEYWDS 7 NUCLEOPROTEIN, VIRION, ZINC-FINGER, VIRAL PROTEIN, HYDROLASE- KEYWDS 8 HYDROLASE INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.BHATTACHARYA,H.ZHANG,A.K.DEBNATH,D.COWBURN REVDAT 5 29-DEC-10 2K1C 1 OBSLTE REVDAT 4 24-FEB-09 2K1C 1 VERSN REVDAT 3 24-JUN-08 2K1C 1 JRNL REVDAT 2 29-APR-08 2K1C 1 JRNL REMARK REVDAT 1 15-APR-08 2K1C 0 JRNL AUTH S.BHATTACHARYA,H.ZHANG,A.K.DEBNATH,D.COWBURN JRNL TITL SOLUTION STRUCTURE OF A HYDROCARBON STAPLED PEPTIDE JRNL TITL 2 INHIBITOR IN COMPLEX WITH MONOMERIC C-TERMINAL DOMAIN OF JRNL TITL 3 HIV-1 CAPSID. JRNL REF J.BIOL.CHEM. V. 283 16274 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18417468 JRNL DOI 10.1074/JBC.C800048200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.ZHANG,Q.ZHAO,S.BHATTACHARYA,A.A.WAHEED,X.TONG,A.HONG, REMARK 1 AUTH 2 S.HECK,F.CURRELI,M.GOGER,D.COWBURN,E.O.FREED,A.K.DEBNATH REMARK 1 TITL A CELL-PENETRATING HELICAL PEPTIDE AS A POTENTIAL HIV-1 REMARK 1 TITL 2 INHIBITOR. REMARK 1 REF J.MOL.BIOL. 2008 REMARK 1 REFN ESSN 1089-8638 REMARK 1 PMID 18374356 REMARK 1 DOI 10.1016/J.JMB.2008.02.066 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTOMATIC NOE ASSIGNMENTS IN CYANA 2.1, REMARK 3 STRUCTURES CALCULATED AND WATER REFINED IN ARIA 2.2. REMARK 4 REMARK 4 2K1C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-08. REMARK 100 THE RCSB ID CODE IS RCSB100551. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 600 UM [U-100% 13C; U-100% 15N] REMARK 210 HIV-1 CAPSID PROTEIN, 900 UM REMARK 210 PEPTIDE INHIBITOR, 90% H2O, 10% REMARK 210 D2O; 600 UM HIV-1 CAPSID PROTEIN, REMARK 210 900 UM PEPTIDE INHIBITOR, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D_15N,13C_F2_FILTERED_NOESY; 3D_13C_F2_SEPARATED_15N,13C_ REMARK 210 F1_FILTERED_NOESY; 3D HNCO; 3D HNCA; 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 -HN(CA)CO; 2D 1H-15N HSQC; 3D HBHA(CO)NH; 3D HN(CO)CA; 3D H(CCO) REMARK 210 NH; 2D 1H-13C HSQC; 2D_15N/13C_F1F2_FILTERED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, TOPSPIN 1.3, CARA REMARK 210 1.5, TALOS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 SER A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 SER A 137 REMARK 465 SER A 138 REMARK 465 GLY A 139 REMARK 465 LEU A 140 REMARK 465 VAL A 141 REMARK 465 PRO A 142 REMARK 465 ARG A 143 REMARK 465 GLY A 144 REMARK 465 SER A 145 REMARK 465 HIS A 146 REMARK 465 MET A 147 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 HG12 ILE A 150 HD23 LEU A 172 1.47 REMARK 500 HH TYR A 169 H14 L2A B 4 1.49 REMARK 500 HG21 THR B 2 H PHE B 3 1.53 REMARK 500 OD2 ASP A 163 HH12 ARG A 167 1.60 REMARK 500 HZ2 LYS A 227 OXT LEU A 231 1.63 REMARK 500 O LEU A 172 HZ3 LYS A 182 1.68 REMARK 500 O LYS A 182 HG1 THR A 186 1.68 REMARK 500 O THR A 216 HE21 GLN A 219 1.70 REMARK 500 O SER A 178 H LYS A 182 1.71 REMARK 500 H ILE A 150 OE2 GLU A 175 1.72 REMARK 500 O MET A 214 H CYS A 218 1.73 REMARK 500 O PRO A 196 HG1 THR A 200 1.74 REMARK 500 O VAL A 165 H TYR A 169 1.76 REMARK 500 O1 L2A B 4 H TYR B 9 1.76 REMARK 500 OD1 ASP A 166 HZ3 LYS A 170 1.77 REMARK 500 OD1 ASN A 183 HN L2A B 4 1.78 REMARK 500 H2 ILE B 1 O2 L2A B 4 1.79 REMARK 500 O PHE A 168 H LEU A 172 1.79 REMARK 500 HE ARG A 229 O LEU A 231 1.81 REMARK 500 O THR A 210 H MET A 214 1.82 REMARK 500 O ASP A 166 HG2 LYS A 170 1.82 REMARK 500 O ASN A 195 H LYS A 199 1.82 REMARK 500 O ILE A 201 H LEU A 205 1.84 REMARK 500 O4 L2A B 4 H TYR B 10 1.84 REMARK 500 O GLN A 179 H ASN A 183 1.85 REMARK 500 O LYS A 182 H THR A 186 1.86 REMARK 500 O GLN A 179 HD21 ASN A 183 1.88 REMARK 500 O THR A 186 H LEU A 190 1.90 REMARK 500 O LEU A 205 H ALA A 208 1.91 REMARK 500 OH TYR A 169 HZ3 LYS B 12 1.92 REMARK 500 O ALA A 185 HG LEU A 189 1.94 REMARK 500 O SER A 149 H ASP A 152 1.94 REMARK 500 O VAL A 191 HE2 LYS A 199 1.95 REMARK 500 O LYS A 199 H LYS A 203 1.99 REMARK 500 O ASN A 183 HG3 GLU A 187 1.99 REMARK 500 O ALA A 185 H LEU A 189 1.99 REMARK 500 O PRO A 160 H TYR A 164 2.01 REMARK 500 O ARG A 167 H THR A 171 2.01 REMARK 500 O TYR A 169 H ARG A 173 2.02 REMARK 500 O PRO A 196 H THR A 200 2.03 REMARK 500 H GLN A 155 O ASN A 193 2.04 REMARK 500 O THR A 171 H ALA A 174 2.05 REMARK 500 O VAL A 221 H GLY A 223 2.06 REMARK 500 O GLN A 155 HD22 ASN A 195 2.07 REMARK 500 O VAL A 181 H ALA A 185 2.08 REMARK 500 O PHE A 161 H VAL A 165 2.08 REMARK 500 O THR A 210 HG3 MET A 214 2.08 REMARK 500 O ASN A 183 H GLU A 187 2.09 REMARK 500 O ARG A 162 H ASP A 166 2.11 REMARK 500 O CYS A 198 HG LEU A 202 2.11 REMARK 500 REMARK 500 THIS ENTRY HAS 1335 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 149 84.21 66.24 REMARK 500 1 ILE A 153 98.99 -69.14 REMARK 500 1 GLN A 176 89.51 -67.84 REMARK 500 1 THR B 2 -66.55 -165.41 REMARK 500 2 ASN A 193 30.24 -89.87 REMARK 500 2 THR B 2 -168.71 -119.83 REMARK 500 3 ILE A 150 -33.55 177.48 REMARK 500 3 HIS A 226 -133.54 56.63 REMARK 500 3 LYS A 227 -145.98 63.11 REMARK 500 3 THR B 2 -41.15 -175.93 REMARK 500 4 GLN A 176 95.02 -69.08 REMARK 500 4 ALA A 177 142.29 -175.34 REMARK 500 4 ALA A 209 -159.25 -128.52 REMARK 500 4 HIS A 226 -67.98 70.93 REMARK 500 4 LYS A 227 69.37 61.64 REMARK 500 5 ALA A 209 -156.57 -154.94 REMARK 500 5 THR B 2 -88.29 -161.54 REMARK 500 6 VAL A 221 81.85 58.48 REMARK 500 6 THR B 2 -173.96 65.06 REMARK 500 6 LYS B 12 91.48 76.99 REMARK 500 7 ALA A 228 75.70 -111.00 REMARK 500 7 THR B 2 -178.92 67.38 REMARK 500 8 ILE A 150 -32.56 65.07 REMARK 500 8 ILE A 153 99.85 -69.55 REMARK 500 8 LYS A 158 29.20 -144.66 REMARK 500 8 ARG A 229 76.71 -105.83 REMARK 500 8 THR B 2 -163.34 58.45 REMARK 500 9 ALA A 209 -153.60 -130.83 REMARK 500 9 ARG A 229 48.00 -83.55 REMARK 500 9 VAL A 230 -77.59 -131.41 REMARK 500 10 ILE A 150 -28.00 64.67 REMARK 500 10 ASN A 193 32.58 -96.35 REMARK 500 10 VAL A 221 95.23 62.01 REMARK 500 10 LYS A 227 125.40 68.41 REMARK 500 10 ALA A 228 32.95 -93.93 REMARK 500 10 THR B 2 -117.00 57.66 REMARK 500 11 SER A 149 -72.97 75.18 REMARK 500 11 LYS A 158 14.44 -141.23 REMARK 500 11 GLN A 176 94.61 -64.42 REMARK 500 11 HIS A 226 74.26 59.27 REMARK 500 11 LYS A 227 34.86 -161.85 REMARK 500 11 THR B 2 -154.57 -142.90 REMARK 500 12 ALA A 228 157.46 66.96 REMARK 500 12 THR B 2 -60.87 -138.10 REMARK 500 13 HIS A 226 53.40 -118.76 REMARK 500 13 ALA A 228 14.09 -150.15 REMARK 500 13 THR B 2 -98.68 -126.16 REMARK 500 13 LYS B 12 53.12 -100.31 REMARK 500 14 ILE A 153 97.03 -67.59 REMARK 500 15 SER A 149 100.27 68.60 REMARK 500 REMARK 500 THIS ENTRY HAS 75 RAMACHANDRAN OUTLIERS. 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 L2A B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L2A B 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15675 RELATED DB: BMRB DBREF 2K1C A 148 231 UNP P35963 POL_HV1Y2 280 363 DBREF 2K1C B 1 14 PDB 2K1C 2K1C 1 14 SEQADV 2K1C MET A 127 UNP P35963 EXPRESSION TAG SEQADV 2K1C GLY A 128 UNP P35963 EXPRESSION TAG SEQADV 2K1C SER A 129 UNP P35963 EXPRESSION TAG SEQADV 2K1C SER A 130 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 131 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 132 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 133 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 134 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 135 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 136 UNP P35963 EXPRESSION TAG SEQADV 2K1C SER A 137 UNP P35963 EXPRESSION TAG SEQADV 2K1C SER A 138 UNP P35963 EXPRESSION TAG SEQADV 2K1C GLY A 139 UNP P35963 EXPRESSION TAG SEQADV 2K1C LEU A 140 UNP P35963 EXPRESSION TAG SEQADV 2K1C VAL A 141 UNP P35963 EXPRESSION TAG SEQADV 2K1C PRO A 142 UNP P35963 EXPRESSION TAG SEQADV 2K1C ARG A 143 UNP P35963 EXPRESSION TAG SEQADV 2K1C GLY A 144 UNP P35963 EXPRESSION TAG SEQADV 2K1C SER A 145 UNP P35963 EXPRESSION TAG SEQADV 2K1C HIS A 146 UNP P35963 EXPRESSION TAG SEQADV 2K1C MET A 147 UNP P35963 EXPRESSION TAG SEQADV 2K1C ALA A 184 UNP P35963 TRP 316 ENGINEERED SEQADV 2K1C ALA A 185 UNP P35963 MET 317 ENGINEERED SEQRES 1 A 105 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 105 LEU VAL PRO ARG GLY SER HIS MET THR SER ILE LEU ASP SEQRES 3 A 105 ILE ARG GLN GLY PRO LYS GLU PRO PHE ARG ASP TYR VAL SEQRES 4 A 105 ASP ARG PHE TYR LYS THR LEU ARG ALA GLU GLN ALA SER SEQRES 5 A 105 GLN GLU VAL LYS ASN ALA ALA THR GLU THR LEU LEU VAL SEQRES 6 A 105 GLN ASN ALA ASN PRO ASP CYS LYS THR ILE LEU LYS ALA SEQRES 7 A 105 LEU GLY PRO ALA ALA THR LEU GLU GLU MET MET THR ALA SEQRES 8 A 105 CYS GLN GLY VAL GLY GLY PRO GLY HIS LYS ALA ARG VAL SEQRES 9 A 105 LEU SEQRES 1 B 10 ILE THR PHE L2A TYR TYR GLY LYS LYS LYS HET L2A B 4 90 HETNAM L2A (2S,5S,8S,11S,15E,20S)-20-AMINO-2-(CARBOXYMETHYL)-11, HETNAM 2 L2A 20-DIMETHYL-5,8-BIS(2-METHYLPROPYL)-3,6,9,21-TETRAOXO- HETNAM 3 L2A 1,4,7,10-TETRAAZACYCLOHENICOS-15-ENE-11-CARBOXYLIC HETNAM 4 L2A ACID FORMUL 2 L2A C30 H51 N5 O8 HELIX 1 1 SER A 149 ILE A 153 5 5 HELIX 2 2 PRO A 160 ARG A 173 1 14 HELIX 3 3 SER A 178 ASN A 193 1 16 HELIX 4 4 ASN A 195 GLY A 206 1 12 HELIX 5 5 PRO A 207 ALA A 209 5 3 HELIX 6 6 THR A 210 CYS A 218 1 9 HELIX 7 7 GLN A 219 VAL A 221 5 3 HELIX 8 8 THR B 2 TYR B 10 1 5 LINK C PHE B 3 N L2A B 4 1555 1555 1.33 LINK C22 L2A B 4 N TYR B 9 1555 1555 1.33 SITE 1 AC1 5 TYR A 169 GLN A 179 GLU A 180 ASN A 183 SITE 2 AC1 5 ILE B 1 SITE 1 AC2 4 ILE B 1 TYR B 9 TYR B 10 GLY B 11 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