HEADER HYDROLASE/HYDROLASE INHIBITOR 27-OCT-09 3KF0 TITLE HIV PROTEASE WITH FRAGMENT 4D9 BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: 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: R8; SOURCE 6 GENE: 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 21A+ KEYWDS PROTEASE, TL-3 INHIBITOR, FRAGMENT HIT, ASPARTYL PROTEASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.D.STOUT,A.L.PERRYMAN REVDAT 6 06-SEP-23 3KF0 1 REMARK REVDAT 5 13-OCT-21 3KF0 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3KF0 1 VERSN REVDAT 3 13-APR-11 3KF0 1 HEADER HETATM HETNAM HETSYN REVDAT 3 2 1 JRNL KEYWDS LINK REMARK REVDAT 2 07-APR-10 3KF0 1 AUTHOR JRNL REVDAT 1 23-FEB-10 3KF0 0 JRNL AUTH A.L.PERRYMAN,Q.ZHANG,H.H.SOUTTER,R.ROSENFELD,D.E.MCREE, JRNL AUTH 2 A.J.OLSON,J.E.ELDER,C.DAVID STOUT JRNL TITL FRAGMENT-BASED SCREEN AGAINST HIV PROTEASE. JRNL REF CHEM.BIOL.DRUG DES. V. 75 257 2010 JRNL REFN ISSN 1747-0277 JRNL PMID 20659109 JRNL DOI 10.1111/J.1747-0285.2009.00943.X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0090 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) : 31.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 21566 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 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) : 1162 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.82000 REMARK 3 B22 (A**2) : -1.75000 REMARK 3 B33 (A**2) : -1.06000 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.079 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1829 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2801 ; 1.064 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 5.336 ; 7.500 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 54 ;43.324 ;24.815 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 288 ;11.346 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.615 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 257 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1984 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 977 ; 0.669 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1588 ; 1.262 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 656 ; 1.932 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 615 ; 3.360 ; 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 : NULL 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; U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3KF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : MONOCHROMATOR:SIDE SCATTERING REMARK 200 BENT CUBE-ROOT I-BEAM SINGLE REMARK 200 CRYSTAL; ASYMMETRIC CUT 4.965 REMARK 200 DEGS; REMARK 200 OPTICS : MONOCHROMATOR:SIDE SCATTERING REMARK 200 BENT CUBE-ROOT I-BEAM SINGLE REMARK 200 CRYSTAL; ASYMMETRIC CUT 4.965 REMARK 200 DEGS; MIRRORS: RH COATED FLAT REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 31.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 5.5000 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18300 REMARK 200 R SYM FOR SHELL (I) : 0.18300 REMARK 200 FOR SHELL : 3.800 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: DIMER GENERATED FROM PDB ENTRY 2AZ8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M KSCN, 0.1 M MES-HCL, PH 5.8, 10% REMARK 280 DMSO, VAPOR DIFFUSION, TEMPERATURE 277.0K 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 29.75900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.95500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.75900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.95500 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: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 349 LIES ON A SPECIAL POSITION. 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 GLU B 35 126.92 -37.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 307 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 94 O REMARK 620 2 THR A 96 OG1 101.5 REMARK 620 3 ASN B 98 O 66.9 74.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 306 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 98 O REMARK 620 2 GLY B 94 O 74.1 REMARK 620 3 THR B 96 OG1 76.5 108.3 REMARK 620 N 1 2 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: BENZYL [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-DIBENZYL- REMARK 630 8,9-DIHYDROXY-1,16-DIMETHYL-4,13-BIS(1-METHYLETHYL)-2,5,12,15,18- REMARK 630 PENTAOXO-20-PHENYL-19-OXA-3,6,11,14,17-PENTAAZAICOS-1-YL]CARBAMATE 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 3TL A 200 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ ALA VAL PHL PHL VAL ALA PHQ 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 3TL A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4DX A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AZ8 RELATED DB: PDB REMARK 900 HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE REMARK 900 RELATED ID: 2AZ9 RELATED DB: PDB REMARK 900 HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, 1X MUTANT REMARK 900 RELATED ID: 2AZB RELATED DB: PDB REMARK 900 HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, 3X MUTANT REMARK 900 RELATED ID: 2AZC RELATED DB: PDB REMARK 900 HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, 6X MUTANT REMARK 900 RELATED ID: 3KF1 RELATED DB: PDB REMARK 900 HIV PROTEASE (PR) DIMER WITHOUT INHIBITOR; ACETATE IN EXO SITE REMARK 900 RELATED ID: 3KFN RELATED DB: PDB REMARK 900 HIV PROTEASE (PR) WITH INHIBITOR TL-3 AND FRAGMENT HIT 4D9 BY REMARK 900 SOAKING REMARK 900 RELATED ID: 3KFP RELATED DB: PDB REMARK 900 HIV PROTEASE (PR) WITH INHIBITOR TL-3 BOUND, AND DMSOS IN EXO SITE REMARK 900 RELATED ID: 3KFR RELATED DB: PDB REMARK 900 HIV PROTEASE (PR) DIMER WITH INHIBITOR TL-3 BOUND AND FRAGMENT 1F1 REMARK 900 IN THE OUTSIDE/TOP OF FLAP REMARK 900 RELATED ID: 3KFS RELATED DB: PDB REMARK 900 HIV PROTEASE (PR) DIMER WITH INHIBITOR TL-3 BOUND AND FRAGMENT 2F4 REMARK 900 IN THE OUTSIDE/TOP OF FLAP DBREF 3KF0 A 1 99 UNP Q903N5 Q903N5_9HIV1 1 99 DBREF 3KF0 B 1 99 UNP Q903N5 Q903N5_9HIV1 1 99 SEQADV 3KF0 LYS A 7 UNP Q903N5 ARG 7 ENGINEERED MUTATION SEQADV 3KF0 LYS B 7 UNP Q903N5 ARG 7 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 LEU GLU GLU MET ASN 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 LEU 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 LEU GLU GLU MET ASN 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 LEU 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 3TL A 200 66 HET 4DX A 201 8 HET DMS A 301 4 HET DMS A 304 4 HET DMS A 305 4 HET K A 307 1 HET BME B 300 4 HET K B 306 1 HETNAM 3TL BENZYL [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-DIBENZYL-8,9- HETNAM 2 3TL DIHYDROXY-1,16-DIMETHYL-4,13-BIS(1-METHYLETHYL)-2,5, HETNAM 3 3TL 12,15,18-PENTAOXO-20-PHENYL-19-OXA-3,6,11,14,17- HETNAM 4 3TL PENTAAZAICOS-1-YL]CARBAMATE HETNAM 4DX (1S,2S)-2-METHYLCYCLOHEXANOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM K POTASSIUM ION HETNAM BME BETA-MERCAPTOETHANOL HETSYN 3TL TL-3, C2 SYMMETRIC INHIBITOR HETSYN 4DX TRANS-2-METHYLCYCLOHEXANOL FORMUL 3 3TL C50 H64 N6 O10 FORMUL 4 4DX C7 H14 O FORMUL 5 DMS 3(C2 H6 O S) FORMUL 8 K 2(K 1+) FORMUL 9 BME C2 H6 O S FORMUL 11 HOH *211(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 GLY B 94 1 9 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 VAL A 56 N LYS A 45 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 LEU 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 LYS 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 GLY B 78 -1 O HIS B 69 N ILE B 66 SHEET 4 C 8 VAL B 32 GLU B 34 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 VAL B 11 O ALA B 22 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 LINK O GLY A 94 K K A 307 1555 1555 2.97 LINK OG1 THR A 96 K K A 307 1555 1555 2.98 LINK O ASN A 98 K K B 306 1555 1555 2.95 LINK K K A 307 O ASN B 98 1555 1555 3.20 LINK O GLY B 94 K K B 306 1555 1555 2.83 LINK OG1 THR B 96 K K B 306 1555 1555 3.07 SITE 1 AC1 26 TRP A 6 ARG A 8 ASP A 25 GLY A 27 SITE 2 AC1 26 ALA A 28 ASP A 29 GLY A 48 GLY A 49 SITE 3 AC1 26 ILE A 50 PHE A 53 PRO A 81 VAL A 82 SITE 4 AC1 26 HOH A 306 HOH A 383 ARG B 8 ASP B 25 SITE 5 AC1 26 GLY B 27 ALA B 28 ASP B 29 GLY B 48 SITE 6 AC1 26 GLY B 49 PHE B 53 PRO B 81 VAL B 82 SITE 7 AC1 26 ILE B 84 HOH B 204 SITE 1 AC2 8 LYS A 14 ILE A 15 GLY A 16 GLY A 17 SITE 2 AC2 8 LEU A 63 ILE A 64 GLU A 65 HOH A 334 SITE 1 AC3 5 THR A 12 GLU A 65 ILE A 66 CYS A 67 SITE 2 AC3 5 GLY A 68 SITE 1 AC4 4 GLY A 73 THR A 74 ASN A 88 ARG B 41 SITE 1 AC5 6 ARG A 87 ASN A 88 THR A 91 LEU B 5 SITE 2 AC5 6 TRP B 6 ARG B 41 SITE 1 AC6 3 GLY A 94 THR A 96 ASN B 98 SITE 1 AC7 6 GLN A 18 MET A 36 ASN A 37 THR B 12 SITE 2 AC7 6 GLU B 65 GLY B 68 SITE 1 AC8 3 ASN A 98 GLY B 94 THR B 96 CRYST1 59.518 85.910 46.440 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 0.016802 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021533 0.00000