HEADER VIRAL PROTEIN/INHIBITOR 18-NOV-10 2L6E TITLE NMR STRUCTURE OF THE MONOMERIC MUTANT C-TERMINAL DOMAIN OF HIV-1 TITLE 2 CAPSID IN COMPLEX WITH STAPLED 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 STAPLED 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; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET14B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS PROTEIN-STAPLED PEPTIDE COMPLEX, VIRAL PROTEIN - PEPTIDE INHIBITOR KEYWDS 2 COMPLEX, VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.BHATTACHARYA,H.ZHANG,A.K.DEBNATH,D.COWBURN REVDAT 3 16-OCT-24 2L6E 1 REMARK REVDAT 2 15-NOV-23 2L6E 1 REMARK SEQADV LINK ATOM REVDAT 1 29-DEC-10 2L6E 0 SPRSDE 29-DEC-10 2L6E 2K1C 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, ARIA 2.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT REMARK 4 REMARK 4 2L6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000102014. 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 : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 600 UM [U-100% 13C; U-100% 15N] REMARK 210 CAPSID PROTEIN P24, 900 UM NYAD- REMARK 210 13 PEPTIDE INHIBITOR, 2 MM DTT, REMARK 210 100 MM AMMONIUM ACETATE, 90% H2O/ REMARK 210 10% D2O; 600 UM [U-100% 13C; U- REMARK 210 100% 15N] CAPSID PROTEIN P24, REMARK 210 900 UM NYAD-13 PEPTIDE INHIBITOR, REMARK 210 2 MM DTT, 100 MM AMMONIUM REMARK 210 ACETATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 2D REMARK 210 F1,F2 FILTERED 1H-1H NOESY; 2D REMARK 210 F2 FILTERED 1H-1H NOESY; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.5, TOPSPIN 1.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 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 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE [(5S)-5-[[(2S)-6-AZANIUMYL-2-[[(2S)-6-AZANIUMYL-2-[2-[[(2S)-2- REMARK 400 [[(2S)-2-[[(2S,5S,8S,11S,20S)-20-[[(2S)-2-[[(2S,3R)-2-[[(2S,3S)-2- REMARK 400 AZANYL-3-METHYL-PENTANOYL]AMINO]-3-OXIDANYL-BUTANOYL]AMINO]-3- REMARK 400 PHENYL-PROPANOYL]AMINO]-2-(2-HYDROXY-2-OXOETHYL)-11,20-DIMETHYL-5,8- REMARK 400 BIS(2-METHYLPROPYL)-3,6,9,21-TETRAKIS(OXIDANYLIDENE)-1,4,7,10- REMARK 400 TETRAZACYCLOHENICOS-11-YL]CARBONYLAMINO]-3-(4-HYDROXYPHENYL) REMARK 400 PROPANOYL]AMINO]-3-(4-HYDROXYPHENYL)PROPANOYL]AMINO]ETHANOYLAMINO] REMARK 400 HEXANOYL]AMINO]HEXANOYL]AMINO]-6-OXIDANYL-6-OXIDANYLIDENE-HEXYL] REMARK 400 AZANIUM IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: [(5S)-5-[[(2S)-6-AZANIUMYL-2-[[(2S)-6-AZANIUMYL-2-[2-[[(2S)- REMARK 400 2-[[(2S)-2-[[(2S,5S,8S,11S,20S)-20-[[(2S)-2-[[(2S,3R)-2- REMARK 400 [[(2S,3S)-2-AZANYL-3-METHYL-PENTANOYL]AMINO]-3-OXIDANYL- REMARK 400 BUTANOYL]AMINO]-3-PHENYL-PROPANOYL]AMINO]-2-(2-HYDROXY-2- REMARK 400 OXOETHYL)-11,20-DIMETHYL-5,8-BIS(2-METHYLPROPYL)-3,6,9,21- REMARK 400 TETRAKIS(OXIDANYLIDENE)-1,4,7,10-TETRAZACYCLOHENICOS-11-YL] REMARK 400 CARBONYLAMINO]-3-(4-HYDROXYPHENYL)PROPANOYL]AMINO]-3-(4- REMARK 400 HYDROXYPHENYL)PROPANOYL]AMINO]ETHANOYLAMINO]HEXANOYL]AMINO] REMARK 400 HEXANOYL]AMINO]-6-OXIDANYL-6-OXIDANYLIDENE-HEXYL]AZANIUM REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 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 HE2 GLU A 159 HH12 ARG A 167 1.31 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 MET A 147 45.74 -169.93 REMARK 500 1 SER A 149 40.89 -164.33 REMARK 500 1 LYS A 227 88.76 61.83 REMARK 500 1 LYS B 12 -158.94 -125.30 REMARK 500 1 LYS B 13 39.32 -144.26 REMARK 500 2 VAL A 141 78.01 37.95 REMARK 500 2 SER A 145 -78.94 62.84 REMARK 500 2 SER A 149 82.56 53.11 REMARK 500 2 PRO A 224 96.54 -54.06 REMARK 500 2 THR B 2 164.19 50.24 REMARK 500 2 LYS B 12 86.53 -69.48 REMARK 500 2 LYS B 13 -153.99 41.97 REMARK 500 3 SER A 145 -166.81 72.64 REMARK 500 3 HIS A 146 -77.83 68.65 REMARK 500 3 THR A 148 -104.16 45.70 REMARK 500 3 SER A 149 81.85 56.22 REMARK 500 4 ARG A 143 22.42 -148.04 REMARK 500 4 SER A 145 -18.48 -169.26 REMARK 500 4 PRO A 224 42.43 -78.21 REMARK 500 4 HIS A 226 -83.21 63.93 REMARK 500 4 ALA A 228 -66.47 68.46 REMARK 500 4 LYS B 13 -77.52 -113.29 REMARK 500 5 SER A 149 57.35 -118.90 REMARK 500 5 ILE A 150 -48.80 57.80 REMARK 500 5 VAL A 221 -68.05 -131.62 REMARK 500 5 VAL A 230 111.08 79.19 REMARK 500 5 THR B 2 140.59 -35.23 REMARK 500 6 LEU A 140 99.88 -68.26 REMARK 500 6 VAL A 141 82.44 51.93 REMARK 500 6 PRO A 142 82.70 -66.93 REMARK 500 6 ARG A 143 -59.98 -160.73 REMARK 500 6 MET A 147 -87.70 -120.73 REMARK 500 6 PRO A 224 112.42 -39.60 REMARK 500 6 ALA A 228 -90.03 -128.40 REMARK 500 6 ARG A 229 -81.44 -108.03 REMARK 500 7 LEU A 140 85.03 56.75 REMARK 500 7 THR A 148 73.66 -150.93 REMARK 500 7 HIS A 226 101.95 63.57 REMARK 500 7 ALA A 228 -165.41 -168.63 REMARK 500 7 ARG A 229 66.50 71.40 REMARK 500 8 LEU A 140 95.19 60.16 REMARK 500 8 HIS A 146 153.42 67.97 REMARK 500 8 MET A 147 -37.87 73.53 REMARK 500 8 PRO A 224 31.64 -89.04 REMARK 500 8 HIS A 226 -59.94 -120.02 REMARK 500 8 VAL A 230 63.92 62.98 REMARK 500 8 THR B 2 163.70 44.67 REMARK 500 8 LYS B 12 -69.35 -143.94 REMARK 500 9 SER A 149 -34.53 178.77 REMARK 500 9 ILE A 150 -32.76 60.70 REMARK 500 REMARK 500 THIS ENTRY HAS 104 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 CHAIN B OF NYAD-13 STAPLED REMARK 800 PEPTIDE INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SIDE CHAINS OF MK8 RESIDUE OF CHAIN B AND NUMBERS 4 AND 8 ARE REMARK 999 LINKED BY A DOUBLE BOND AT THE CE ATOMS. DBREF 2L6E A 148 231 UNP P35963 POL_HV1Y2 280 363 DBREF 2L6E B 1 14 PDB 2L6E 2L6E 1 14 SEQADV 2L6E MET A 127 UNP P35963 INITIATING METHIONINE SEQADV 2L6E GLY A 128 UNP P35963 EXPRESSION TAG SEQADV 2L6E SER A 129 UNP P35963 EXPRESSION TAG SEQADV 2L6E SER A 130 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 131 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 132 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 133 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 134 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 135 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 136 UNP P35963 EXPRESSION TAG SEQADV 2L6E SER A 137 UNP P35963 EXPRESSION TAG SEQADV 2L6E SER A 138 UNP P35963 EXPRESSION TAG SEQADV 2L6E GLY A 139 UNP P35963 EXPRESSION TAG SEQADV 2L6E LEU A 140 UNP P35963 EXPRESSION TAG SEQADV 2L6E VAL A 141 UNP P35963 EXPRESSION TAG SEQADV 2L6E PRO A 142 UNP P35963 EXPRESSION TAG SEQADV 2L6E ARG A 143 UNP P35963 EXPRESSION TAG SEQADV 2L6E GLY A 144 UNP P35963 EXPRESSION TAG SEQADV 2L6E SER A 145 UNP P35963 EXPRESSION TAG SEQADV 2L6E HIS A 146 UNP P35963 EXPRESSION TAG SEQADV 2L6E MET A 147 UNP P35963 EXPRESSION TAG SEQADV 2L6E ALA A 184 UNP P35963 TRP 316 ENGINEERED MUTATION SEQADV 2L6E ALA A 185 UNP P35963 MET 317 ENGINEERED MUTATION 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 14 ILE THR PHE MK8 ASP LEU LEU MK8 TYR TYR GLY LYS LYS SEQRES 2 B 14 LYS MODRES 2L6E MK8 B 4 LEU 2-METHYL-L-NORLEUCINE MODRES 2L6E MK8 B 8 LEU 2-METHYL-L-NORLEUCINE HET MK8 B 4 20 HET MK8 B 8 20 HETNAM MK8 2-METHYL-L-NORLEUCINE FORMUL 2 MK8 2(C7 H15 N O2) HELIX 1 1 SER A 149 ILE A 153 5 5 HELIX 2 2 PRO A 160 ALA A 174 1 15 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 THR A 210 CYS A 218 1 9 HELIX 6 6 THR B 2 LYS B 12 1 11 LINK C PHE B 3 N MK8 B 4 1555 1555 1.34 LINK C MK8 B 4 N ASP B 5 1555 1555 1.34 LINK CE MK8 B 4 CE MK8 B 8 1555 1555 1.39 LINK C LEU B 7 N MK8 B 8 1555 1555 1.34 LINK C MK8 B 8 N TYR B 9 1555 1555 1.32 SITE 1 AC1 13 VAL A 165 ASP A 166 TYR A 169 LEU A 172 SITE 2 AC1 13 ARG A 173 ASN A 183 THR A 186 GLU A 187 SITE 3 AC1 13 ALA A 209 THR A 210 LEU A 211 GLU A 212 SITE 4 AC1 13 MET A 215 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