HEADER HYDROLASE 16-OCT-07 2RKF TITLE HIV-1 PR RESISTANT MUTANT + LPV 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 STRAIN: TYPE B; SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET LIKE, T7 PROMOTOR DRIVEN KEYWDS RESISTENCE, INSERTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.REZACOVA,J.BRYNDA,M.KOZISEK,K.G.SASKOVA,J.KONVALINKA REVDAT 5 30-AUG-23 2RKF 1 REMARK REVDAT 4 20-OCT-21 2RKF 1 REMARK SEQADV HETSYN REVDAT 3 13-JUL-11 2RKF 1 VERSN REVDAT 2 24-FEB-09 2RKF 1 VERSN REVDAT 1 05-AUG-08 2RKF 0 JRNL AUTH M.KOZISEK,K.G.SASKOVA,P.REZACOVA,J.BRYNDA, JRNL AUTH 2 N.M.VAN MAARSEVEEN,D.DE JONG,C.A.BOUCHER,R.M.KAGAN, JRNL AUTH 3 M.NIJHUIS,J.KONVALINKA JRNL TITL NINETY-NINE IS NOT ENOUGH: MOLECULAR CHARACTERIZATION OF JRNL TITL 2 INHIBITOR-RESISTANT HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 JRNL TITL 3 PROTEASE MUTANTS WITH INSERTIONS IN THE FLAP REGION JRNL REF J.VIROL. V. 82 5869 2008 JRNL REFN ISSN 0022-538X JRNL PMID 18400858 JRNL DOI 10.1128/JVI.02325-07 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15673 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1236 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1102 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1511 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 26.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.878 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1761 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2411 ; 1.455 ; 2.032 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 5.541 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 65 ;41.250 ;24.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 289 ;12.114 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;12.766 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1307 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 787 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1201 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 130 ; 0.141 ; 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): 59 ; 0.216 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.158 ; 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): 1069 ; 0.932 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1685 ; 1.308 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 791 ; 1.677 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 716 ; 2.452 ; 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 99 4 REMARK 3 1 B 1 B 99 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 753 ; 0.42 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 753 ; 0.39 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 501 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 B (A): 46 ; 0.02 ; 0.05 REMARK 3 TIGHT THERMAL 2 B (A**2): 46 ; 0.05 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 9 REMARK 3 RESIDUE RANGE : A 86 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): -32.3800 2.8230 1.1610 REMARK 3 T TENSOR REMARK 3 T11: -0.1494 T22: -0.1815 REMARK 3 T33: -0.1388 T12: 0.0079 REMARK 3 T13: 0.0003 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 2.4905 L22: 2.0694 REMARK 3 L33: 6.8549 L12: 0.4165 REMARK 3 L13: 0.6092 L23: 2.1629 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: -0.0389 S13: 0.1020 REMARK 3 S21: -0.0576 S22: -0.2182 S23: 0.1606 REMARK 3 S31: -0.1759 S32: -0.6306 S33: 0.1825 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 9 REMARK 3 RESIDUE RANGE : B 86 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): -32.4510 -2.6940 -1.8430 REMARK 3 T TENSOR REMARK 3 T11: -0.1599 T22: -0.1785 REMARK 3 T33: -0.1370 T12: -0.0035 REMARK 3 T13: -0.0089 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 2.1926 L22: 2.4901 REMARK 3 L33: 9.0291 L12: -0.2409 REMARK 3 L13: -1.1182 L23: 1.7750 REMARK 3 S TENSOR REMARK 3 S11: 0.0174 S12: 0.0675 S13: -0.0754 REMARK 3 S21: 0.0236 S22: -0.2383 S23: 0.1244 REMARK 3 S31: 0.0649 S32: -0.6377 S33: 0.2209 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 32 REMARK 3 RESIDUE RANGE : A 63 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): -24.3750 9.2450 8.8570 REMARK 3 T TENSOR REMARK 3 T11: -0.1003 T22: -0.1240 REMARK 3 T33: -0.0772 T12: -0.0151 REMARK 3 T13: 0.0002 T23: -0.0461 REMARK 3 L TENSOR REMARK 3 L11: 1.0442 L22: 5.1283 REMARK 3 L33: 3.2149 L12: -0.8327 REMARK 3 L13: 0.0226 L23: 1.7222 REMARK 3 S TENSOR REMARK 3 S11: 0.0328 S12: -0.1588 S13: 0.1081 REMARK 3 S21: 0.0747 S22: 0.0102 S23: -0.2123 REMARK 3 S31: -0.0152 S32: 0.1135 S33: -0.0430 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 10 B 32 REMARK 3 RESIDUE RANGE : B 63 B 85 REMARK 3 ORIGIN FOR THE GROUP (A): -24.3800 -9.2590 -9.5020 REMARK 3 T TENSOR REMARK 3 T11: -0.0999 T22: -0.1334 REMARK 3 T33: -0.0779 T12: 0.0202 REMARK 3 T13: 0.0024 T23: -0.0484 REMARK 3 L TENSOR REMARK 3 L11: 1.0504 L22: 5.3156 REMARK 3 L33: 3.3697 L12: 1.0967 REMARK 3 L13: 0.1988 L23: 2.0469 REMARK 3 S TENSOR REMARK 3 S11: 0.0435 S12: 0.1450 S13: -0.1255 REMARK 3 S21: -0.0921 S22: 0.0356 S23: -0.2080 REMARK 3 S31: 0.0336 S32: 0.1112 S33: -0.0791 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 : A 33 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): -13.7290 5.7350 13.9490 REMARK 3 T TENSOR REMARK 3 T11: 0.0290 T22: 0.1195 REMARK 3 T33: 0.1408 T12: 0.0524 REMARK 3 T13: -0.1295 T23: -0.1401 REMARK 3 L TENSOR REMARK 3 L11: 10.6315 L22: 4.4615 REMARK 3 L33: 11.5020 L12: -3.5065 REMARK 3 L13: -6.6747 L23: 1.4196 REMARK 3 S TENSOR REMARK 3 S11: -0.4963 S12: -1.0817 S13: 0.3190 REMARK 3 S21: 0.7004 S22: 0.4962 S23: -0.8022 REMARK 3 S31: 0.4088 S32: 1.0356 S33: 0.0001 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 : B 33 B 62 REMARK 3 ORIGIN FOR THE GROUP (A): -13.7200 -5.6070 -14.5830 REMARK 3 T TENSOR REMARK 3 T11: 0.0421 T22: 0.1215 REMARK 3 T33: 0.1422 T12: -0.0446 REMARK 3 T13: 0.1187 T23: -0.1267 REMARK 3 L TENSOR REMARK 3 L11: 9.0634 L22: 2.4365 REMARK 3 L33: 12.5369 L12: 2.6749 REMARK 3 L13: 6.7789 L23: 0.5964 REMARK 3 S TENSOR REMARK 3 S11: -0.4865 S12: 0.9479 S13: -0.1977 REMARK 3 S21: -0.7251 S22: 0.3871 S23: -0.6776 REMARK 3 S31: -0.3995 S32: 1.0810 S33: 0.0994 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 : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1170 -0.0080 -0.3060 REMARK 3 T TENSOR REMARK 3 T11: -0.0625 T22: -0.0078 REMARK 3 T33: 0.0493 T12: 0.0419 REMARK 3 T13: 0.0039 T23: -0.0591 REMARK 3 L TENSOR REMARK 3 L11: 2.2940 L22: 7.6819 REMARK 3 L33: 8.4406 L12: -0.3831 REMARK 3 L13: 2.7795 L23: -2.7079 REMARK 3 S TENSOR REMARK 3 S11: 0.2424 S12: -0.3384 S13: 0.1048 REMARK 3 S21: -0.7929 S22: 0.1729 S23: -0.2902 REMARK 3 S31: 0.7063 S32: 0.6142 S33: -0.4152 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 : 1.40 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 2RKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000044967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 24.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 37.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37500 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1U8G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR: 0.1M MES PH 5.4, 0.5M REMARK 280 AMMONIUM SULFATE; DROPS: 2UL PROTEIN + 1UL RESERVOIR CPR=8MG/ML, REMARK 280 5-FOLD MOLAR EXCESS OF LPV , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.03533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.07067 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.05300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 70.08833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.01767 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 40 C ARG A 41 N 0.150 REMARK 500 GLY B 40 C GLY B 40 O 0.139 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 PRO B 79 48.17 -70.68 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 SO4 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AB1 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1002 DBREF 2RKF A 1 99 UNP A0F7J4 A0F7J4_9HIV1 1 99 DBREF 2RKF B 1 99 UNP A0F7J4 A0F7J4_9HIV1 1 99 SEQADV 2RKF VAL A 13 UNP A0F7J4 ILE 13 ENGINEERED MUTATION SEQADV 2RKF ALA A 16 UNP A0F7J4 GLY 16 ENGINEERED MUTATION SEQADV 2RKF MET A 20 UNP A0F7J4 LYS 20 ENGINEERED MUTATION SEQADV 2RKF SER A 37 UNP A0F7J4 ASN 37 ENGINEERED MUTATION SEQADV 2RKF VAL A 46 UNP A0F7J4 ILE 46 ENGINEERED MUTATION SEQADV 2RKF MET A 54 UNP A0F7J4 LEU 54 ENGINEERED MUTATION SEQADV 2RKF LEU A 63 UNP A0F7J4 PRO 63 ENGINEERED MUTATION SEQADV 2RKF ILE A 93 UNP A0F7J4 LEU 93 ENGINEERED MUTATION SEQADV 2RKF VAL B 13 UNP A0F7J4 ILE 13 ENGINEERED MUTATION SEQADV 2RKF ALA B 16 UNP A0F7J4 GLY 16 ENGINEERED MUTATION SEQADV 2RKF MET B 20 UNP A0F7J4 LYS 20 ENGINEERED MUTATION SEQADV 2RKF SER B 37 UNP A0F7J4 ASN 37 ENGINEERED MUTATION SEQADV 2RKF VAL B 46 UNP A0F7J4 ILE 46 ENGINEERED MUTATION SEQADV 2RKF MET B 54 UNP A0F7J4 LEU 54 ENGINEERED MUTATION SEQADV 2RKF LEU B 63 UNP A0F7J4 PRO 63 ENGINEERED MUTATION SEQADV 2RKF ILE B 93 UNP A0F7J4 LEU 93 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP GLN ARG PRO PHE VAL THR VAL SEQRES 2 A 99 LYS ILE ALA GLY GLN LEU MET GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR ILE LEU GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG TRP THR PRO LYS VAL VAL GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE MET LYS VAL ARG GLN TYR ASP GLN ILE LEU VAL GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO ALA 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 GLN ARG PRO PHE VAL THR VAL SEQRES 2 B 99 LYS ILE ALA GLY GLN LEU MET GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR ILE LEU GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG TRP THR PRO LYS VAL VAL GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE MET LYS VAL ARG GLN TYR ASP GLN ILE LEU VAL GLU SEQRES 6 B 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO ALA ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE HET SO4 A2001 5 HET AB1 A 501 92 HET GOL A1001 6 HET SO4 B2002 5 HET GOL B1002 6 HETNAM SO4 SULFATE ION HETNAM AB1 N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3- HETNAM 2 AB1 HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO- HETNAM 3 AB1 PYRIMIDIN-1-YL)-BUTYRAMIDE HETNAM GOL GLYCEROL HETSYN AB1 ABT-378; LOPINAVIR HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 AB1 C37 H48 N4 O5 FORMUL 5 GOL 2(C3 H8 O3) FORMUL 8 HOH *132(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLN A 92 GLY A 94 5 3 HELIX 3 3 GLY B 86 THR B 91 1 6 HELIX 4 4 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 THR B 4 -1 O ILE B 3 N LEU A 97 SHEET 1 B 8 THR A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O VAL A 56 N LYS A 45 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O VAL A 71 N VAL A 64 SHEET 4 B 8 ILE 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 ILE 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 PHE A 10 ILE A 15 -1 N VAL A 13 O MET A 20 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 C 8 THR B 43 GLY B 49 0 SHEET 2 C 8 GLY B 52 ILE B 66 -1 O VAL B 56 N LYS B 45 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O VAL B 75 N TYR B 59 SHEET 4 C 8 ILE 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 ILE 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 PHE B 10 ILE B 15 -1 N VAL B 13 O MET B 20 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SITE 1 AC1 3 GLN A 7 ARG A 8 HOH A2020 SITE 1 AC2 4 ARG A 8 GLN B 7 ARG B 8 HOH B2035 SITE 1 AC3 27 LEU A 23 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC3 27 ASP A 29 ASP A 30 ILE A 32 GLY A 48 SITE 3 AC3 27 GLY A 49 ILE A 50 PRO A 81 ALA A 82 SITE 4 AC3 27 HOH A2002 HOH A2003 HOH A2004 HOH A2005 SITE 5 AC3 27 LEU B 23 ASP B 25 GLY B 27 ALA B 28 SITE 6 AC3 27 ASP B 29 ASP B 30 ILE B 32 GLY B 48 SITE 7 AC3 27 GLY B 49 ALA B 82 ILE B 84 SITE 1 AC4 4 ASP A 29 ARG A 87 ASN A 88 TRP B 6 SITE 1 AC5 4 TRP A 6 ASP B 29 ARG B 87 HOH B2061 CRYST1 61.961 61.961 84.106 90.00 90.00 120.00 P 61 12 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 0.016139 0.009318 0.000000 0.00000 SCALE2 0.000000 0.018636 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011890 0.00000