HEADER HYDROLASE 06-OCT-99 1D4Y TITLE HIV-1 PROTEASE TRIPLE MUTANT/TIPRANAVIR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HIV-1 PROTEASE); COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HUMAN IMMUNODEFICIENCY VIRUS TYPE 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_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, ACID PROTEASE, ASPARTYL PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR K.D.WATENPAUGH,M.N.JANAKIRAMAN REVDAT 7 07-FEB-24 1D4Y 1 REMARK REVDAT 6 03-NOV-21 1D4Y 1 REMARK SEQADV REVDAT 5 04-OCT-17 1D4Y 1 REMARK REVDAT 4 22-FEB-12 1D4Y 1 JRNL VERSN REVDAT 3 24-FEB-09 1D4Y 1 VERSN REVDAT 2 01-APR-03 1D4Y 1 JRNL REVDAT 1 13-OCT-99 1D4Y 0 JRNL AUTH S.THAISRIVONGS,H.I.SKULNICK,S.R.TURNER,J.W.STROHBACH, JRNL AUTH 2 R.A.TOMMASI,P.D.JOHNSON,P.A.ARISTOFF,T.M.JUDGE,R.B.GAMMILL, JRNL AUTH 3 J.K.MORRIS,K.R.ROMINES,R.A.CHRUSCIEL,R.R.HINSHAW,K.T.CHONG, JRNL AUTH 4 W.G.TARPLEY,S.M.POPPE,D.E.SLADE,J.C.LYNN,M.M.HORNG, JRNL AUTH 5 P.K.TOMICH,E.P.SEEST,L.A.DOLAK,W.J.HOWE,G.M.HOWARD, JRNL AUTH 6 K.D.WATENPAUGH JRNL TITL STRUCTURE-BASED DESIGN OF HIV PROTEASE INHIBITORS: JRNL TITL 2 SULFONAMIDE-CONTAINING 5,6-DIHYDRO-4-HYDROXY-2-PYRONES AS JRNL TITL 3 NON-PEPTIDIC INHIBITORS. JRNL REF J.MED.CHEM. V. 39 4349 1996 JRNL REFN ISSN 0022-2623 JRNL PMID 8893827 JRNL DOI 10.1021/JM960541S REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.175 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.174 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 763 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 15278 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1488 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009798. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 5.4 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 : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 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 (%) : 90.0 REMARK 200 DATA REDUNDANCY : 7.230 REMARK 200 R MERGE (I) : 0.07510 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.31700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.89250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.75150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.89250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.75150 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: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 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 14 CD CE NZ REMARK 470 ARG A 41 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 70 CD CE NZ REMARK 470 LYS B 7 CE NZ REMARK 470 GLN B 18 CG CD OE1 NE2 REMARK 470 LYS B 55 CD CE NZ REMARK 470 LYS B 70 CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPV A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D4S RELATED DB: PDB DBREF 1D4Y A 1 99 UNP P03367 POL_HV1BR 69 167 DBREF 1D4Y B 1 99 UNP P03367 POL_HV1BR 69 167 SEQADV 1D4Y LYS A 7 UNP P03367 GLN 75 ENGINEERED MUTATION SEQADV 1D4Y ILE A 33 UNP P03367 LEU 101 ENGINEERED MUTATION SEQADV 1D4Y ILE A 63 UNP P03367 LEU 131 ENGINEERED MUTATION SEQADV 1D4Y LYS B 7 UNP P03367 GLN 75 ENGINEERED MUTATION SEQADV 1D4Y ILE B 33 UNP P03367 LEU 101 ENGINEERED MUTATION SEQADV 1D4Y ILE B 63 UNP P03367 LEU 131 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG 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 ILE 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 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG 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 ILE 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 HET TPV A 501 42 HETNAM TPV N-(3-{(1R)-1-[(6R)-4-HYDROXY-2-OXO-6-PHENETHYL-6- HETNAM 2 TPV PROPYL-5,6-DIHYDRO-2H-PYRAN-3-YL]PROPYL}PHENYL)-5- HETNAM 3 TPV (TRIFLUOROMETHYL)-2-PYRIDINESULFONAMIDE HETSYN TPV TIPRANAVIR FORMUL 3 TPV C31 H33 F3 N2 O5 S FORMUL 4 HOH *207(H2 O) HELIX 1 H1 GLY A 86 THR A 91 1 6 HELIX 2 H2 GLY B 86 THR B 91 1 6 SHEET 1 S1 4 PRO A 1 LEU A 5 0 SHEET 2 S1 4 CYS B 95 PHE B 99 -1 O LEU B 97 N ILE A 3 SHEET 3 S1 4 CYS A 95 PHE A 99 -1 O THR A 96 N ASN B 98 SHEET 4 S1 4 PRO B 1 LEU B 5 -1 O ILE B 3 N LEU A 97 SHEET 1 S2 2 PRO A 9 ILE A 15 0 SHEET 2 S2 2 GLN A 18 LEU A 24 -1 N LEU A 24 O PRO A 9 SHEET 1 S3 3 ALA A 22 LEU A 24 0 SHEET 2 S3 3 ASN A 83 GLY A 86 1 O ASN A 83 N LEU A 23 SHEET 3 S3 3 ASP A 30 VAL A 32 -1 N VAL A 32 O ILE A 84 SHEET 1 S4 3 LYS A 43 GLY A 48 0 SHEET 2 S4 3 GLY A 52 TYR A 59 -1 N ILE A 54 O ILE A 47 SHEET 3 S4 3 VAL A 75 VAL A 77 -1 O VAL A 75 N TYR A 59 SHEET 1 S5 2 PRO B 9 ILE B 15 0 SHEET 2 S5 2 GLN B 18 LEU B 24 -1 N LEU B 24 O PRO B 9 SHEET 1 S6 3 ALA B 22 LEU B 24 0 SHEET 2 S6 3 ASN B 83 GLY B 86 1 O ASN B 83 N LEU B 23 SHEET 3 S6 3 ASP B 30 VAL B 32 -1 N VAL B 32 O ILE B 84 SHEET 1 S7 3 LYS B 43 GLY B 48 0 SHEET 2 S7 3 GLY B 52 TYR B 59 -1 N ILE B 54 O ILE B 47 SHEET 3 S7 3 VAL B 75 VAL B 77 -1 O VAL B 75 N TYR B 59 SITE 1 AC1 21 LEU A 23 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC1 21 ASP A 29 ASP A 30 ILE A 47 GLY A 48 SITE 3 AC1 21 GLY A 49 ILE A 50 VAL A 82 HOH A 507 SITE 4 AC1 21 HOH A 572 ARG B 8 LEU B 23 ASP B 25 SITE 5 AC1 21 GLY B 49 ILE B 50 VAL B 82 ILE B 84 SITE 6 AC1 21 HOH B 206 CRYST1 59.785 87.503 46.458 90.00 90.00 90.00 P 21 21 2 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 0.016727 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021525 0.00000