HEADER HYDROLASE/HYDROLASE INHIBITOR 19-SEP-08 3EKQ TITLE CRYSTAL STRUCTURE OF INHIBITOR SAQUINAVIR (SQV) IN COMPLEX WITH MULTI- TITLE 2 DRUG RESISTANT HIV-1 PROTEASE (L63P/V82T/I84V) (REFERRED TO AS ACT IN TITLE 3 PAPER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 491-589; COMPND 5 SYNONYM: RETROPEPSIN, PR; COMPND 6 EC: 3.4.23.16; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV-1 M:B_ARV2/SF2; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11685; SOURCE 5 STRAIN: HXB2; SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: TAP106; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PXC35 KEYWDS PROTEASE INHIBITOR, DRUG RESISTANCE, ENTROPY ENTHALPY COMPENSATION, KEYWDS 2 AIDS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PRABU-JEYABALAN,N.M.KING,C.A.SCHIFFER,E.NALIVAIKA REVDAT 7 30-AUG-23 3EKQ 1 REMARK REVDAT 6 20-OCT-21 3EKQ 1 COMPND REMARK SEQADV HETNAM REVDAT 6 2 1 HETSYN REVDAT 5 25-OCT-17 3EKQ 1 REMARK REVDAT 4 17-OCT-12 3EKQ 1 JRNL REVDAT 3 25-JUL-12 3EKQ 1 JRNL REVDAT 2 13-JUL-11 3EKQ 1 VERSN REVDAT 1 01-SEP-09 3EKQ 0 JRNL AUTH N.M.KING,M.PRABU-JEYABALAN,R.M.BANDARANAYAKE,M.N.NALAM, JRNL AUTH 2 E.A.NALIVAIKA,A.OZEN,N.K.YILMAZ,C.A.SCHIFFER JRNL TITL EXTREME ENTROPY-ENTHALPY COMPENSATION IN A DRUG-RESISTANT JRNL TITL 2 VARIANT OF HIV-1 PROTEASE. JRNL REF ACS CHEM.BIOL. V. 7 1536 2012 JRNL REFN ISSN 1554-8929 JRNL PMID 22712830 JRNL DOI 10.1021/CB300191K REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 9751 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 467 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 594 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.14000 REMARK 3 B22 (A**2) : -1.19000 REMARK 3 B33 (A**2) : 2.33000 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): 0.334 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.232 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.182 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1583 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1523 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2170 ; 1.273 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3527 ; 0.714 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 200 ; 6.953 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;40.441 ;25.098 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 246 ;13.593 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;14.060 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 259 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1723 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 285 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 208 ; 0.179 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1478 ; 0.205 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 719 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 888 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 64 ; 0.158 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.032 ; 0.200 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): 6 ; 0.167 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 46 ; 0.147 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.072 ; 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): 1276 ; 1.063 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 414 ; 0.124 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1610 ; 1.022 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 704 ; 1.660 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 560 ; 2.212 ; 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 : 10 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 : B 1 B 5 REMARK 3 RESIDUE RANGE : A 94 A 99 REMARK 3 RESIDUE RANGE : B 94 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): 20.2272 8.9636 2.5108 REMARK 3 T TENSOR REMARK 3 T11: 0.0031 T22: 0.0052 REMARK 3 T33: -0.0972 T12: -0.0802 REMARK 3 T13: -0.0645 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 4.2750 L22: 7.5149 REMARK 3 L33: 0.4083 L12: 2.7027 REMARK 3 L13: 0.0999 L23: 0.0582 REMARK 3 S TENSOR REMARK 3 S11: -0.1426 S12: 0.4732 S13: 0.4162 REMARK 3 S21: -0.6332 S22: 0.1385 S23: 0.2435 REMARK 3 S31: -0.0172 S32: -0.2500 S33: 0.0041 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 86 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): 28.6078 9.4922 12.1298 REMARK 3 T TENSOR REMARK 3 T11: -0.0144 T22: -0.0315 REMARK 3 T33: -0.0329 T12: -0.0178 REMARK 3 T13: 0.0087 T23: -0.0242 REMARK 3 L TENSOR REMARK 3 L11: 12.2035 L22: 1.9351 REMARK 3 L33: 0.4661 L12: -3.3844 REMARK 3 L13: -1.7160 L23: 0.0026 REMARK 3 S TENSOR REMARK 3 S11: -0.3962 S12: -0.5679 S13: 0.2745 REMARK 3 S21: 0.0146 S22: 0.4136 S23: -0.2390 REMARK 3 S31: 0.1819 S32: 0.0818 S33: -0.0174 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 86 B 92 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9680 -0.3245 4.8674 REMARK 3 T TENSOR REMARK 3 T11: -0.0746 T22: 0.0677 REMARK 3 T33: -0.0914 T12: -0.0544 REMARK 3 T13: -0.0396 T23: -0.0622 REMARK 3 L TENSOR REMARK 3 L11: 5.6208 L22: 4.9133 REMARK 3 L33: 0.4786 L12: 3.9950 REMARK 3 L13: 0.4607 L23: -0.6287 REMARK 3 S TENSOR REMARK 3 S11: -0.4040 S12: 0.7706 S13: -0.2739 REMARK 3 S21: -0.1703 S22: 0.0743 S23: 0.5712 REMARK 3 S31: 0.6178 S32: -0.3841 S33: 0.3297 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 44 A 55 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8005 -1.0047 26.3472 REMARK 3 T TENSOR REMARK 3 T11: -0.0306 T22: -0.0166 REMARK 3 T33: -0.1221 T12: -0.0220 REMARK 3 T13: 0.0220 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 29.3749 L22: 11.8391 REMARK 3 L33: 1.4732 L12: 10.6233 REMARK 3 L13: 6.4842 L23: 1.7662 REMARK 3 S TENSOR REMARK 3 S11: 0.4616 S12: -1.2747 S13: 0.0634 REMARK 3 S21: 0.7436 S22: -0.5552 S23: 0.3759 REMARK 3 S31: 0.2606 S32: -0.4565 S33: 0.0936 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 44 B 55 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2521 -10.5785 19.4980 REMARK 3 T TENSOR REMARK 3 T11: -0.1038 T22: -0.0995 REMARK 3 T33: 0.0997 T12: -0.0132 REMARK 3 T13: -0.0092 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 5.9051 L22: 5.9736 REMARK 3 L33: 1.5150 L12: 2.5366 REMARK 3 L13: 1.1991 L23: 1.4423 REMARK 3 S TENSOR REMARK 3 S11: 0.1515 S12: -0.1992 S13: -0.0003 REMARK 3 S21: 0.5143 S22: 0.0201 S23: 0.5660 REMARK 3 S31: 0.1758 S32: 0.1678 S33: -0.1716 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 77 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): 29.8621 -3.7834 16.4627 REMARK 3 T TENSOR REMARK 3 T11: -0.0365 T22: -0.0468 REMARK 3 T33: 0.0199 T12: -0.0016 REMARK 3 T13: -0.0070 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 3.0926 L22: 3.5720 REMARK 3 L33: 0.0923 L12: -1.5678 REMARK 3 L13: 0.4809 L23: -0.0234 REMARK 3 S TENSOR REMARK 3 S11: 0.0157 S12: -0.1459 S13: -0.0576 REMARK 3 S21: -0.1341 S22: -0.1082 S23: 0.0422 REMARK 3 S31: 0.4332 S32: -0.0342 S33: 0.0925 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 77 B 85 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5478 0.0829 18.9099 REMARK 3 T TENSOR REMARK 3 T11: 0.0227 T22: -0.0329 REMARK 3 T33: 0.0325 T12: -0.0725 REMARK 3 T13: 0.0208 T23: 0.0838 REMARK 3 L TENSOR REMARK 3 L11: 6.8730 L22: 13.0735 REMARK 3 L33: 1.1971 L12: -2.5731 REMARK 3 L13: 1.0216 L23: 3.1754 REMARK 3 S TENSOR REMARK 3 S11: 0.2038 S12: -0.7587 S13: -0.3951 REMARK 3 S21: 1.7455 S22: 0.0516 S23: 0.8200 REMARK 3 S31: -0.7089 S32: 0.1804 S33: -0.2554 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 24 A 31 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1494 4.2495 13.2486 REMARK 3 T TENSOR REMARK 3 T11: -0.0681 T22: -0.0146 REMARK 3 T33: 0.0200 T12: -0.0066 REMARK 3 T13: -0.0096 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 7.1636 L22: 5.1256 REMARK 3 L33: 0.2599 L12: -0.2318 REMARK 3 L13: -0.6286 L23: -1.0033 REMARK 3 S TENSOR REMARK 3 S11: 0.0024 S12: -0.1041 S13: -0.1785 REMARK 3 S21: 0.0514 S22: -0.0220 S23: 0.2198 REMARK 3 S31: -0.0443 S32: 0.1894 S33: 0.0196 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 : B 24 B 31 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3081 0.4111 10.2496 REMARK 3 T TENSOR REMARK 3 T11: -0.0442 T22: -0.0238 REMARK 3 T33: -0.0551 T12: 0.0104 REMARK 3 T13: -0.0115 T23: -0.0614 REMARK 3 L TENSOR REMARK 3 L11: 10.0186 L22: 5.1849 REMARK 3 L33: 0.1461 L12: -2.4333 REMARK 3 L13: 1.1927 L23: -0.4274 REMARK 3 S TENSOR REMARK 3 S11: -0.2772 S12: -0.0540 S13: -0.1564 REMARK 3 S21: -0.2057 S22: -0.0564 S23: -0.0484 REMARK 3 S31: 0.0836 S32: -0.0302 S33: 0.3336 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 100 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): 19.8884 -0.5903 18.0082 REMARK 3 T TENSOR REMARK 3 T11: 0.0603 T22: 0.0664 REMARK 3 T33: 0.1203 T12: -0.0297 REMARK 3 T13: -0.0120 T23: 0.0922 REMARK 3 L TENSOR REMARK 3 L11: 20.5527 L22: 13.4555 REMARK 3 L33: 0.3596 L12: -3.1504 REMARK 3 L13: -0.2268 L23: -2.1177 REMARK 3 S TENSOR REMARK 3 S11: -0.2209 S12: -0.9087 S13: -0.7591 REMARK 3 S21: 0.4887 S22: 0.4670 S23: 0.8363 REMARK 3 S31: -0.5022 S32: 0.3530 S33: -0.2461 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3EKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 300 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 MIRRORS REMARK 200 OPTICS : YALE MIRRORS 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 : 12975 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 6.0000 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1F7A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 300K 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 25.58200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.69450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.64550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.69450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.58200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.64550 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 300 REMARK: ONE DIMER (A & B IDENTIFIERS) IN ONE ASYMMETRIC UNIT 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL 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 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 41 CG CD CE NZ REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 THR A 82 OG1 CG2 REMARK 470 LYS B 7 CG CD CE NZ REMARK 470 ARG B 14 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 37 CG OD1 ND2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 THR B 82 OG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 14 NE CZ NH1 NH2 REMARK 480 GLU B 35 CD OE1 OE2 REMARK 480 GLN B 61 CD OE1 NE2 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 79 49.36 -79.30 REMARK 500 GLU B 34 174.24 -55.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR ROC IS A HYDROXYETHYLAMINE CONTAINING REMARK 600 TRANSITION STATE MIMETIC. REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT- REMARK 630 BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3- REMARK 630 HYDROXY-1 -PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO) REMARK 630 BUTANEDIAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 ROC A 100 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: QNC ASN HP0 NTB REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ROC A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EKP RELATED DB: PDB REMARK 900 RELATED ID: 3EKT RELATED DB: PDB REMARK 900 RELATED ID: 3EKV RELATED DB: PDB REMARK 900 RELATED ID: 3EKW RELATED DB: PDB REMARK 900 RELATED ID: 3EKX RELATED DB: PDB REMARK 900 RELATED ID: 3EKY RELATED DB: PDB REMARK 900 RELATED ID: 3EL0 RELATED DB: PDB REMARK 900 RELATED ID: 3EL4 RELATED DB: PDB REMARK 900 RELATED ID: 3EL5 RELATED DB: PDB REMARK 900 RELATED ID: 3EM3 RELATED DB: PDB REMARK 900 RELATED ID: 3EM4 RELATED DB: PDB REMARK 900 RELATED ID: 3EM6 RELATED DB: PDB DBREF 3EKQ A 1 99 UNP P03369 POL_HV1A2 491 589 DBREF 3EKQ B 1 99 UNP P03369 POL_HV1A2 491 589 SEQADV 3EKQ LYS A 7 UNP P03369 GLN 497 ENGINEERED MUTATION SEQADV 3EKQ ILE A 10 UNP P03369 LEU 500 ENGINEERED MUTATION SEQADV 3EKQ VAL A 48 UNP P03369 GLY 538 ENGINEERED MUTATION SEQADV 3EKQ VAL A 54 UNP P03369 ILE 544 ENGINEERED MUTATION SEQADV 3EKQ ILE A 64 UNP P03369 VAL 554 ENGINEERED MUTATION SEQADV 3EKQ THR A 82 UNP P03369 VAL 572 ENGINEERED MUTATION SEQADV 3EKQ LYS B 7 UNP P03369 GLN 497 ENGINEERED MUTATION SEQADV 3EKQ ILE B 10 UNP P03369 LEU 500 ENGINEERED MUTATION SEQADV 3EKQ VAL B 48 UNP P03369 GLY 538 ENGINEERED MUTATION SEQADV 3EKQ VAL B 54 UNP P03369 ILE 544 ENGINEERED MUTATION SEQADV 3EKQ ILE B 64 UNP P03369 VAL 554 ENGINEERED MUTATION SEQADV 3EKQ THR B 82 UNP P03369 VAL 572 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO ILE VAL THR ILE SEQRES 2 A 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP 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 VAL GLY ILE GLY GLY SEQRES 5 A 99 PHE VAL 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 THR 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 ILE VAL THR ILE SEQRES 2 B 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP 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 VAL GLY ILE GLY GLY SEQRES 5 B 99 PHE VAL 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 THR ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE HET ROC A 100 49 HET PO4 A 502 5 HET PO4 B 501 5 HETNAM ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT- HETNAM 2 ROC BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H- HETNAM 3 ROC ISOQUINOLIN-2-YL]-3-HYDROXY-1 -PHENYL-BUTAN-2-YL]-2- HETNAM 4 ROC (QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE HETNAM PO4 PHOSPHATE ION HETSYN ROC FORTOVASE; SAQUINAVIR; RO 31-8959 FORMUL 3 ROC C38 H50 N6 O5 FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 HOH *74(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 HELIX 3 3 GLN B 92 GLY B 94 5 3 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 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 B 8 LYS A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 B 8 VAL A 32 LEU A 33 1 N LEU A 33 O LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 B 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 B 8 ILE A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 B 8 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 ALA B 71 N ILE B 64 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 ILE 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 SITE 1 AC1 19 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 19 ASP A 30 VAL A 48 GLY A 49 ILE A 50 SITE 3 AC1 19 THR A 80 HOH A 507 HOH A 509 HOH A 549 SITE 4 AC1 19 ARG B 8 LEU B 23 ASP B 25 GLY B 27 SITE 5 AC1 19 VAL B 48 ILE B 50 PRO B 81 SITE 1 AC2 2 LYS A 7 ARG A 8 SITE 1 AC3 4 LYS B 20 GLU B 21 ASN B 83 HOH B 511 CRYST1 51.164 59.291 61.389 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 0.019545 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016866 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016290 0.00000