HEADER HYDROLASE/HYDROLASE SUBSTRATE 17-NOV-06 2NXM TITLE STRUCTURE OF HIV-1 PROTEASE D25N COMPLEXED WITH THE RT-RH ANALOGUE TITLE 2 PEPTIDE GLY-ALA-GLN-THR-PHE*TYR-VAL-ASP-GLY-ALA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE RETROPEPSIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HIV-1 PROTEASE; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ANALOGUE OF RT-RH POL PROTEASE SUBSTRATE PEPTIDE; COMPND 10 CHAIN: P; COMPND 11 FRAGMENT: DECAPEPTIDE FRAGMENT; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV-1 M:B_ARV2/SF2; SOURCE 3 ORGANISM_TAXID: 11685; SOURCE 4 STRAIN: SF2; SOURCE 5 GENE: POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TAP106; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PXC35; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS SEQUENCE WAS CUSTOM-DESIGNED AND THEN PURCHASED SOURCE 14 COMMERCIALLY KEYWDS PEPTIDE DESIGN; MOLECULAR DYNAMICS; HIV PROTEASE; SUBSTRATE KEYWDS 2 RECOGNITION; CALORIMETRY, HYDROLASE-HYDROLASE SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.PRABU-JEYABALAN,E.NALIVAIKA,C.A.SCHIFFER REVDAT 6 30-AUG-23 2NXM 1 REMARK REVDAT 5 20-OCT-21 2NXM 1 SEQADV REVDAT 4 18-OCT-17 2NXM 1 REMARK REVDAT 3 24-FEB-09 2NXM 1 VERSN REVDAT 2 15-JAN-08 2NXM 1 JRNL REVDAT 1 18-SEP-07 2NXM 0 JRNL AUTH M.D.ALTMAN,E.A.NALIVAIKA,M.PRABU-JEYABALAN,C.A.SCHIFFER, JRNL AUTH 2 B.TIDOR JRNL TITL COMPUTATIONAL DESIGN AND EXPERIMENTAL STUDY OF TIGHTER JRNL TITL 2 BINDING PEPTIDES TO AN INACTIVATED MUTANT OF HIV-1 PROTEASE JRNL REF PROTEINS V. 70 678 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17729291 JRNL DOI 10.1002/PROT.21514 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 8037 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 405 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 389 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 20 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.47000 REMARK 3 B22 (A**2) : 1.91000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.444 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.257 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.860 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1571 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2142 ; 1.264 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 203 ; 7.224 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;39.553 ;24.828 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 253 ;15.778 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 9.234 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 256 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1163 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 640 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1071 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 85 ; 0.157 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.171 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.202 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1040 ; 0.946 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1640 ; 1.378 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 597 ; 2.147 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 502 ; 3.141 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 17 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 5 REMARK 3 RESIDUE RANGE : A 94 A 99 REMARK 3 RESIDUE RANGE : B 1 B 5 REMARK 3 RESIDUE RANGE : B 94 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): 4.8380 8.9278 28.8866 REMARK 3 T TENSOR REMARK 3 T11: 0.0637 T22: -0.0228 REMARK 3 T33: -0.0512 T12: 0.0397 REMARK 3 T13: -0.0224 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 3.3038 L22: 1.1316 REMARK 3 L33: 2.6312 L12: -1.9254 REMARK 3 L13: 1.8571 L23: -0.9596 REMARK 3 S TENSOR REMARK 3 S11: -0.3359 S12: -0.2861 S13: 0.1127 REMARK 3 S21: 0.0557 S22: 0.2569 S23: -0.0177 REMARK 3 S31: -0.2066 S32: -0.0652 S33: 0.0790 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 10 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1418 -3.9031 28.3600 REMARK 3 T TENSOR REMARK 3 T11: 0.0418 T22: -0.0423 REMARK 3 T33: -0.0289 T12: 0.0503 REMARK 3 T13: 0.0008 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 10.9108 L22: 3.3386 REMARK 3 L33: 5.7260 L12: -3.3543 REMARK 3 L13: -3.3722 L23: -2.2507 REMARK 3 S TENSOR REMARK 3 S11: -0.2076 S12: -0.7000 S13: -0.5347 REMARK 3 S21: 0.2937 S22: -0.0066 S23: 0.1775 REMARK 3 S31: -0.0766 S32: -0.5067 S33: 0.2142 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 10 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8912 12.7228 16.6592 REMARK 3 T TENSOR REMARK 3 T11: 0.0460 T22: -0.0901 REMARK 3 T33: 0.0261 T12: -0.0110 REMARK 3 T13: -0.0297 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 7.8682 L22: 0.1106 REMARK 3 L33: 3.0111 L12: 0.6728 REMARK 3 L13: -1.2446 L23: -0.4927 REMARK 3 S TENSOR REMARK 3 S11: 0.0435 S12: 0.0674 S13: 0.6545 REMARK 3 S21: -0.1818 S22: 0.1148 S23: -0.3979 REMARK 3 S31: -0.2426 S32: 0.2595 S33: -0.1583 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 23 A 32 REMARK 3 ORIGIN FOR THE GROUP (A): -0.1364 3.1243 16.9839 REMARK 3 T TENSOR REMARK 3 T11: 0.0245 T22: -0.0006 REMARK 3 T33: -0.0189 T12: -0.0106 REMARK 3 T13: 0.0101 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 4.8481 L22: 1.0788 REMARK 3 L33: 0.1795 L12: 0.9583 REMARK 3 L13: -0.9295 L23: -0.2177 REMARK 3 S TENSOR REMARK 3 S11: -0.0089 S12: 0.2321 S13: 0.0709 REMARK 3 S21: 0.0191 S22: -0.1058 S23: -0.0300 REMARK 3 S31: -0.0133 S32: 0.0812 S33: 0.1147 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 23 B 32 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3139 -0.3507 19.8100 REMARK 3 T TENSOR REMARK 3 T11: -0.0017 T22: -0.0365 REMARK 3 T33: -0.0127 T12: -0.0152 REMARK 3 T13: -0.0196 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 4.7477 L22: 1.5018 REMARK 3 L33: 3.3214 L12: -0.0011 REMARK 3 L13: -1.1723 L23: -0.2177 REMARK 3 S TENSOR REMARK 3 S11: -0.1920 S12: 0.1299 S13: -0.1992 REMARK 3 S21: 0.0408 S22: 0.2168 S23: 0.2580 REMARK 3 S31: -0.0022 S32: 0.0869 S33: -0.0248 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 44 A 55 REMARK 3 ORIGIN FOR THE GROUP (A): -0.4580 -1.5980 3.9605 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: -0.0265 REMARK 3 T33: -0.0665 T12: 0.0045 REMARK 3 T13: 0.0128 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 11.0280 L22: 3.1524 REMARK 3 L33: 0.0100 L12: -0.7613 REMARK 3 L13: -0.3041 L23: 0.0922 REMARK 3 S TENSOR REMARK 3 S11: 0.0558 S12: 0.5638 S13: -0.1663 REMARK 3 S21: -0.4802 S22: -0.1005 S23: -0.2966 REMARK 3 S31: 0.0475 S32: 0.2052 S33: 0.0447 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 44 B 55 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2720 -10.3847 11.3720 REMARK 3 T TENSOR REMARK 3 T11: 0.0231 T22: -0.0182 REMARK 3 T33: -0.0286 T12: 0.0040 REMARK 3 T13: 0.0028 T23: 0.0167 REMARK 3 L TENSOR REMARK 3 L11: 5.8681 L22: 2.5528 REMARK 3 L33: 1.0341 L12: -1.9294 REMARK 3 L13: -0.7576 L23: 1.5893 REMARK 3 S TENSOR REMARK 3 S11: 0.1035 S12: 0.0626 S13: 0.2399 REMARK 3 S21: 0.0452 S22: 0.0274 S23: -0.2763 REMARK 3 S31: -0.1169 S32: -0.1812 S33: -0.1309 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 58 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): -13.6226 6.5415 10.1803 REMARK 3 T TENSOR REMARK 3 T11: -0.0662 T22: 0.0031 REMARK 3 T33: 0.1022 T12: 0.0062 REMARK 3 T13: -0.0073 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 0.3087 L22: 3.6175 REMARK 3 L33: 9.8382 L12: -1.0568 REMARK 3 L13: -1.7428 L23: 5.9657 REMARK 3 S TENSOR REMARK 3 S11: 0.4554 S12: 0.2121 S13: 0.1859 REMARK 3 S21: -0.1880 S22: -0.2374 S23: 0.0192 REMARK 3 S31: 0.1800 S32: -0.5123 S33: -0.2179 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 63 A 68 REMARK 3 ORIGIN FOR THE GROUP (A): -12.1749 5.1515 24.3527 REMARK 3 T TENSOR REMARK 3 T11: 0.0232 T22: -0.0214 REMARK 3 T33: 0.0321 T12: -0.0348 REMARK 3 T13: 0.0337 T23: 0.0592 REMARK 3 L TENSOR REMARK 3 L11: 12.3534 L22: 1.2527 REMARK 3 L33: 2.3033 L12: -1.6704 REMARK 3 L13: 1.0023 L23: 1.3750 REMARK 3 S TENSOR REMARK 3 S11: -0.2883 S12: -0.5165 S13: -0.3693 REMARK 3 S21: 0.3135 S22: -0.0131 S23: 0.2562 REMARK 3 S31: -0.0344 S32: -0.1012 S33: 0.3015 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 69 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): -10.4904 7.5421 17.9070 REMARK 3 T TENSOR REMARK 3 T11: 0.0601 T22: -0.0507 REMARK 3 T33: 0.0041 T12: 0.0007 REMARK 3 T13: 0.0272 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 3.3010 L22: 0.0332 REMARK 3 L33: 0.0400 L12: -0.3309 REMARK 3 L13: 0.3633 L23: -0.0364 REMARK 3 S TENSOR REMARK 3 S11: 0.0212 S12: 0.1788 S13: 0.0532 REMARK 3 S21: 0.1378 S22: -0.2025 S23: 0.0294 REMARK 3 S31: 0.0452 S32: -0.2219 S33: 0.1813 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 58 B 62 REMARK 3 ORIGIN FOR THE GROUP (A): 23.6702 -7.7976 21.2449 REMARK 3 T TENSOR REMARK 3 T11: -0.0608 T22: -0.0232 REMARK 3 T33: 0.0256 T12: 0.0416 REMARK 3 T13: -0.0330 T23: -0.0757 REMARK 3 L TENSOR REMARK 3 L11: 4.9752 L22: 9.6694 REMARK 3 L33: 7.3115 L12: 4.3940 REMARK 3 L13: 0.1937 L23: 2.1314 REMARK 3 S TENSOR REMARK 3 S11: 0.1617 S12: 0.2138 S13: -0.2174 REMARK 3 S21: 0.5526 S22: 0.2288 S23: -0.1192 REMARK 3 S31: 0.5274 S32: 0.3800 S33: -0.3905 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 63 B 68 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0795 6.0322 24.8866 REMARK 3 T TENSOR REMARK 3 T11: -0.0305 T22: -0.0402 REMARK 3 T33: -0.0539 T12: -0.0252 REMARK 3 T13: -0.0263 T23: 0.0606 REMARK 3 L TENSOR REMARK 3 L11: 13.2377 L22: 21.3076 REMARK 3 L33: 8.0468 L12: -7.0288 REMARK 3 L13: -4.2368 L23: 9.6298 REMARK 3 S TENSOR REMARK 3 S11: -0.4454 S12: 0.1662 S13: -0.0415 REMARK 3 S21: 0.2914 S22: 0.3544 S23: 0.5620 REMARK 3 S31: -0.2479 S32: 0.4004 S33: 0.0910 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 69 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): 20.8932 -0.2639 25.0813 REMARK 3 T TENSOR REMARK 3 T11: -0.0024 T22: -0.0200 REMARK 3 T33: 0.0231 T12: 0.0172 REMARK 3 T13: -0.0275 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.4373 L22: 4.7606 REMARK 3 L33: 2.7520 L12: 0.1186 REMARK 3 L13: 0.5109 L23: 3.1573 REMARK 3 S TENSOR REMARK 3 S11: -0.0688 S12: -0.0587 S13: -0.0352 REMARK 3 S21: 0.0978 S22: 0.3042 S23: -0.3041 REMARK 3 S31: 0.1032 S32: 0.4443 S33: -0.2354 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 77 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3625 -4.1147 14.5064 REMARK 3 T TENSOR REMARK 3 T11: 0.0071 T22: -0.0099 REMARK 3 T33: -0.0071 T12: -0.0262 REMARK 3 T13: 0.0014 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 4.0152 L22: 1.6865 REMARK 3 L33: 6.4712 L12: -1.6866 REMARK 3 L13: -3.3702 L23: -0.4717 REMARK 3 S TENSOR REMARK 3 S11: -0.0172 S12: 0.0556 S13: 0.0015 REMARK 3 S21: 0.0208 S22: 0.0009 S23: 0.2011 REMARK 3 S31: 0.4550 S32: 0.1480 S33: 0.0163 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 77 B 85 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0713 0.0694 12.3735 REMARK 3 T TENSOR REMARK 3 T11: 0.0308 T22: 0.0421 REMARK 3 T33: -0.0813 T12: 0.0240 REMARK 3 T13: 0.0216 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 6.6046 L22: 2.0896 REMARK 3 L33: 6.6975 L12: -2.2282 REMARK 3 L13: -2.5080 L23: 3.6185 REMARK 3 S TENSOR REMARK 3 S11: 0.1387 S12: 0.6211 S13: 0.0612 REMARK 3 S21: -0.1032 S22: -0.3285 S23: -0.1013 REMARK 3 S31: -0.3752 S32: -0.3916 S33: 0.1898 REMARK 3 REMARK 3 TLS GROUP : 16 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 86 A 93 REMARK 3 ORIGIN FOR THE GROUP (A): -3.8243 9.9338 19.6344 REMARK 3 T TENSOR REMARK 3 T11: 0.0318 T22: -0.0026 REMARK 3 T33: 0.0048 T12: 0.0003 REMARK 3 T13: -0.0008 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 1.1476 L22: 0.0961 REMARK 3 L33: 0.4313 L12: -0.3321 REMARK 3 L13: 0.7035 L23: -0.2036 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: -0.1449 S13: 0.1786 REMARK 3 S21: -0.0520 S22: 0.0326 S23: -0.0827 REMARK 3 S31: -0.0178 S32: -0.1637 S33: 0.0029 REMARK 3 REMARK 3 TLS GROUP : 17 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 86 B 93 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6561 -0.0785 27.2798 REMARK 3 T TENSOR REMARK 3 T11: -0.0080 T22: 0.0061 REMARK 3 T33: 0.0007 T12: 0.0383 REMARK 3 T13: -0.0194 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.3526 L22: 6.2201 REMARK 3 L33: 4.0467 L12: -0.4443 REMARK 3 L13: 2.1080 L23: 1.4584 REMARK 3 S TENSOR REMARK 3 S11: -0.2703 S12: -0.2648 S13: -0.2845 REMARK 3 S21: 0.0616 S22: 0.2304 S23: -0.0928 REMARK 3 S31: -0.1996 S32: 0.1299 S33: 0.0399 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2NXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE REMARK 200 OPTICS : YALE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8523 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 42.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1T3R - CRYSTAL STRUCTURE OF HIV-1 PROTEASE BOUND REMARK 200 WITH TMC114 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 126MM SODIUM PHOSPHATE PH 6.2; 63MM REMARK 280 SODIUM CITRATE; 25-35% AMMONIUM SULPHATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.53700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.85550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.26750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.85550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.53700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.26750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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, P 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY P 1 REMARK 465 ALA P 10 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 ILE A 50 CG1 CG2 CD1 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS B 7 CG CD CE NZ REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LYS B 55 CG CD CE NZ 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 PRO A 9 75.49 -69.72 REMARK 500 GLU A 34 159.39 -44.02 REMARK 500 ASN B 37 59.44 -92.21 REMARK 500 PHE P 5 47.61 -101.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KJG RELATED DB: PDB REMARK 900 STRUCTURE OF D25N PROTEASE BOUND TO THE RT-RH SUBSTRATE PEPTIDE REMARK 900 RELATED ID: 2NXD RELATED DB: PDB REMARK 900 RELATED ID: 2NXL RELATED DB: PDB DBREF 2NXM A 1 99 UNP O38732 O38732_9HIV1 1 99 DBREF 2NXM B 1 99 UNP O38732 O38732_9HIV1 1 99 DBREF 2NXM P 1 10 PDB 2NXM 2NXM 1 10 SEQADV 2NXM LYS A 7 UNP O38732 GLN 7 ENGINEERED MUTATION SEQADV 2NXM ASN A 25 UNP O38732 ASP 25 ENGINEERED MUTATION SEQADV 2NXM LYS B 7 UNP O38732 GLN 7 ENGINEERED MUTATION SEQADV 2NXM ASN B 25 UNP O38732 ASP 25 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO SEQRES 4 A 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY CYS THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO SEQRES 4 B 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 B 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE SEQRES 1 P 10 GLY ALA GLN THR PHE TYR VAL ASP GLY ALA FORMUL 4 HOH *71(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 A 4 GLN B 2 THR B 4 -1 O ILE B 3 N LEU A 97 SHEET 1 B 9 GLN P 3 THR P 4 0 SHEET 2 B 9 LYS A 43 GLY A 49 1 N GLY A 48 O THR P 4 SHEET 3 B 9 GLY A 52 ILE A 66 -1 O VAL A 56 N LYS A 45 SHEET 4 B 9 HIS A 69 VAL A 77 -1 O VAL A 75 N TYR A 59 SHEET 5 B 9 VAL A 32 LEU A 33 1 N LEU A 33 O LEU A 76 SHEET 6 B 9 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 7 B 9 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 8 B 9 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 9 B 9 GLY A 52 ILE A 66 -1 O GLU A 65 N ARG A 14 SHEET 1 C 8 LYS B 43 GLY B 49 0 SHEET 2 C 8 GLY B 52 ILE B 66 -1 O GLN B 58 N LYS B 43 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O HIS B 69 N ILE B 66 SHEET 4 C 8 VAL B 32 LEU B 33 1 N LEU B 33 O LEU B 76 SHEET 5 C 8 ILE B 84 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 C 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 C 8 LEU B 10 ILE B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N ARG B 14 CRYST1 51.074 58.535 61.711 90.00 90.00 90.00 P 21 21 21 8 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 0.019579 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017084 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016205 0.00000