HEADER HYDROLASE (ACID PROTEASE) 04-MAR-96 4UPJ TITLE HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 TITLE 2 REPLACED BY LEU (K57L) COMPLEX WITH U097410 [4-HYDROXY-3-[1-[3- TITLE 3 [[[[(TERT-BUTYLOXYCARBONYL) TITLE 4 AMINOMETHYL]CARBONYL]AMINO]PHENYL]PROPYL]COUMARIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-2 PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11709; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE (ACID PROTEASE) EXPDTA X-RAY DIFFRACTION AUTHOR K.D.WATENPAUGH,A.M.MULICHAK,M.N.JANAKIRAMAN REVDAT 7 03-APR-24 4UPJ 1 REMARK REVDAT 6 28-FEB-24 4UPJ 1 REMARK REVDAT 5 03-NOV-21 4UPJ 1 REMARK SEQADV REVDAT 4 22-FEB-12 4UPJ 1 JRNL VERSN REVDAT 3 24-FEB-09 4UPJ 1 VERSN REVDAT 2 01-APR-03 4UPJ 1 JRNL REVDAT 1 14-OCT-96 4UPJ 0 JRNL AUTH S.THAISRIVONGS,K.D.WATENPAUGH,W.J.HOWE,P.K.TOMICH,L.A.DOLAK, JRNL AUTH 2 K.-T.CHONG,C.-S.C.TOMICH,A.G.TOMASSELLI,S.R.TURNER, JRNL AUTH 3 J.W.STROHBACH,A.M.MULICHAK,M.N.JANAKIRAMAN,J.B.MOON, JRNL AUTH 4 J.C.LYNN,M.-M.HORNG,R.R.HINSHAW,K.A.CURRY,D.J.ROTHROCK JRNL TITL STRUCTURE-BASED DESIGN OF NOVEL HIV PROTEASE INHIBITORS: JRNL TITL 2 CARBOXAMIDE-CONTAINING 4-HYDROXYCOUMARINS AND JRNL TITL 3 4-HYDROXY-2-PYRONES AS POTENT NONPEPTIDIC INHIBITORS. JRNL REF J.MED.CHEM. V. 38 3624 1995 JRNL REFN ISSN 0022-2623 JRNL PMID 7658450 JRNL DOI 10.1021/JM00018A023 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CEDAR REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10697 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1508 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 2.582 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE IS NO ELECTRON DENSITY BEYOND CB REMARK 3 OF RESIDUE GLU 37. REMARK 4 REMARK 4 4UPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-92 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12378 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: EARLIER STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 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 15.56400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.36750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.65600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.36750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.56400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.65600 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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: 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 ASN A 41 70.36 -101.09 REMARK 500 ASN B 41 75.81 -110.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 REGARDING RESIDUE U04 [THE INHIBITOR]: ATOMS OA2 AND OA3 REMARK 600 ARE, RESPECTIVELY, THE CARBONYL OXYGEN AND RING OXYGEN OF REMARK 600 THE LACTONIC FUNCTION. THE ATOM OA9 IS THE HYDROXYLIC REMARK 600 OXYGEN OF THE COUMARIN TEMPLATE. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U04 A 100 DBREF 4UPJ A 1 99 UNP P04584 POL_HV2RO 86 184 DBREF 4UPJ B 1 99 UNP P04584 POL_HV2RO 86 184 SEQADV 4UPJ LEU A 57 UNP P04584 LYS 142 ENGINEERED MUTATION SEQADV 4UPJ LEU B 57 UNP P04584 LYS 142 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN PHE SER LEU TRP LYS ARG PRO VAL VAL THR ALA SEQRES 2 A 99 TYR ILE GLU GLY GLN PRO VAL GLU VAL LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP SER ILE VAL ALA GLY ILE GLU LEU GLY SEQRES 4 A 99 ASN ASN TYR SER PRO LYS ILE VAL GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE ASN THR LEU GLU TYR LYS ASN VAL GLU ILE GLU SEQRES 6 A 99 VAL LEU ASN LYS LYS VAL ARG ALA THR ILE MET THR GLY SEQRES 7 A 99 ASP THR PRO ILE ASN ILE PHE GLY ARG ASN ILE LEU THR SEQRES 8 A 99 ALA LEU GLY MET SER LEU ASN LEU SEQRES 1 B 99 PRO GLN PHE SER LEU TRP LYS ARG PRO VAL VAL THR ALA SEQRES 2 B 99 TYR ILE GLU GLY GLN PRO VAL GLU VAL LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP SER ILE VAL ALA GLY ILE GLU LEU GLY SEQRES 4 B 99 ASN ASN TYR SER PRO LYS ILE VAL GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE ASN THR LEU GLU TYR LYS ASN VAL GLU ILE GLU SEQRES 6 B 99 VAL LEU ASN LYS LYS VAL ARG ALA THR ILE MET THR GLY SEQRES 7 B 99 ASP THR PRO ILE ASN ILE PHE GLY ARG ASN ILE LEU THR SEQRES 8 B 99 ALA LEU GLY MET SER LEU ASN LEU HET U04 A 100 33 HETNAM U04 ({3-[1-(4-HYDROXY-2-OXO-2H-CHROMEN-3-YL)-PROPYL]- HETNAM 2 U04 PHENYLCARBAMOYL}-METHYL)-CARBAMIC ACID TERT-BUTYL HETNAM 3 U04 ESTER HETSYN U04 U097410 FORMUL 3 U04 C25 H28 N2 O6 FORMUL 4 HOH *176(H2 O) HELIX 1 H1 GLY A 86 LEU A 93 1 8 HELIX 2 H2 GLY B 86 LEU B 93 1 8 SHEET 1 S1 4 PRO A 1 PHE A 3 0 SHEET 2 S1 4 MET B 95 LEU B 99 -1 N LEU B 97 O PHE A 3 SHEET 3 S1 4 MET A 95 LEU A 99 -1 N SER A 96 O ASN B 98 SHEET 4 S1 4 PRO B 1 SER B 4 -1 N PHE B 3 O LEU A 97 SHEET 1 S2 4 GLN A 18 LEU A 24 0 SHEET 2 S2 4 ALA A 13 PRO A 19 -1 N ALA A 13 O VAL A 20 SHEET 3 S2 4 VAL A 62 GLU A 65 -1 N GLU A 65 O TYR A 14 SHEET 4 S2 4 LYS A 69 ALA A 73 -1 N VAL A 71 O ILE A 64 SHEET 1 S3 4 GLN B 18 LEU B 24 0 SHEET 2 S3 4 ALA B 13 PRO B 19 -1 N ALA B 13 O VAL B 20 SHEET 3 S3 4 VAL B 62 GLU B 65 -1 N GLU B 65 O TYR B 14 SHEET 4 S3 4 LYS B 69 ALA B 73 -1 N VAL B 71 O ILE B 64 SITE 1 AC1 18 PRO A 1 ASP A 25 ALA A 28 ASP A 29 SITE 2 AC1 18 ASP A 30 VAL A 47 GLY A 48 GLY A 49 SITE 3 AC1 18 ILE A 50 ILE A 82 ILE A 84 HOH A 434 SITE 4 AC1 18 ARG B 8 ASP B 25 GLY B 27 GLY B 49 SITE 5 AC1 18 ILE B 50 ILE B 84 CRYST1 31.128 45.312 132.735 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 0.032125 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022069 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007534 0.00000