PDB Short entry for 1KJ4 HEADER HYDROLASE 04-DEC-01 1KJ4 TITLE SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR TITLE 2 HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE TITLE 3 COMPLEXES COMPND MOL_ID: 1; COMPND 2 MOLECULE: POL POLYPROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: HIV-1 PROTEASE, RESIDUES 57-155; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: GAG POLYPROTEIN; COMPND 10 CHAIN: P, S; COMPND 11 FRAGMENT: MATRIX-CAPSID SUBSTRATE PEPTIDE, RESIDUES 127-136; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS MARIX-CAPSID, SUBSTRATE RECOGNITION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SCHIFFER REVDAT 5 16-AUG-23 1KJ4 1 REMARK REVDAT 4 27-OCT-21 1KJ4 1 REMARK SEQADV REVDAT 3 24-FEB-09 1KJ4 1 VERSN REVDAT 2 01-APR-03 1KJ4 1 JRNL REVDAT 1 06-MAR-02 1KJ4 0 JRNL AUTH M.PRABU-JEYABALAN,E.NALIVAIKA,C.A.SCHIFFER JRNL TITL SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION FOR JRNL TITL 2 HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX JRNL TITL 3 SUBSTRATE COMPLEXES. JRNL REF STRUCTURE V. 10 369 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12005435 JRNL DOI 10.1016/S0969-2126(02)00720-7 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 64173.540 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 12376 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 SET) : 0.197 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1031 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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 : 3065 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.76000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -2.96000 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 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 69.22 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : ACE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : ACE.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-99 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : NULL 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 : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12376 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 38.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.1000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1F7A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, SODIUM PHOSPHATE, REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.82550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.90400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.08600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.82550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.90400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.08600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.82550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.90400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.08600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.82550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.90400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.08600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: THE ENTIRE BIOLOGICAL DIMER ALONG WITH THE SUBSTRATE REMARK 300 PEPTIDE BOUND IN THE ACTIVE SITE ARE PROVIDED IN THIS COORDINATE REMARK 300 FILE 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, S 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 24-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 67200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -359.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, P, S 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 91.65100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 93.80800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 91.65100 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 118.17200 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 93.80800 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 118.17200 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN P 10 REMARK 465 GLN S 9 REMARK 465 ASN S 10 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 GLN A 2 CG CD OE1 NE2 REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 GLU A 35 CG CD OE1 OE2 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 LYS B 41 CG CD CE NZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 LYS B 55 CG CD CE NZ REMARK 470 GLN B 61 CG CD OE1 NE2 REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 ARG C 14 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 34 CG CD OE1 OE2 REMARK 470 ASN C 37 CG OD1 ND2 REMARK 470 LYS C 41 CG CD CE NZ REMARK 470 LYS C 43 CG CD CE NZ REMARK 470 GLU C 65 CG CD OE1 OE2 REMARK 470 LYS C 70 CG CD CE NZ REMARK 470 LYS D 7 CG CD CE NZ REMARK 470 ASN D 37 CG OD1 ND2 REMARK 470 LYS D 41 CG CD CE NZ REMARK 470 LYS D 43 CG CD CE NZ REMARK 470 LYS D 45 CG CD CE NZ REMARK 470 LYS D 55 CG CD CE NZ REMARK 470 LYS D 70 CG CD CE NZ REMARK 470 GLN P 9 CG 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 GLU A 35 109.32 -18.57 REMARK 500 GLN A 61 71.00 48.58 REMARK 500 LYS B 7 132.59 -175.36 REMARK 500 ARG B 8 112.42 -21.79 REMARK 500 PRO B 9 71.14 -69.97 REMARK 500 LYS B 45 141.61 -177.14 REMARK 500 CYS B 67 39.54 20.40 REMARK 500 ALA B 71 112.88 172.66 REMARK 500 ARG C 8 111.46 -28.55 REMARK 500 PRO C 9 71.32 -67.41 REMARK 500 ASP C 30 -167.21 -109.55 REMARK 500 GLU C 35 106.03 -18.96 REMARK 500 TRP C 42 -167.65 -121.63 REMARK 500 CYS C 67 67.23 36.20 REMARK 500 LEU D 5 39.54 -99.72 REMARK 500 PRO D 9 67.51 -64.76 REMARK 500 GLU D 34 173.88 -54.94 REMARK 500 PRO D 79 46.54 -68.87 REMARK 500 TYR P 5 58.69 -107.14 REMARK 500 TYR S 5 47.81 -108.07 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 ACT B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT D 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 522 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT D 523 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 524 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F7A RELATED DB: PDB REMARK 900 HOW DOES A SYMMETRIC DIMER RECOGNIZE AN ASYMMETRIC SUBSTRATE? A REMARK 900 SUBSTRATE COMPLEX OF HIV-1 PROTEASE REMARK 900 RELATED ID: 1KJ7 RELATED DB: PDB REMARK 900 SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION REMARK 900 FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE REMARK 900 COMPLEXES REMARK 900 RELATED ID: 1KJF RELATED DB: PDB REMARK 900 SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION REMARK 900 FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE REMARK 900 COMPLEXES REMARK 900 RELATED ID: 1KJG RELATED DB: PDB REMARK 900 SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION REMARK 900 FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE REMARK 900 COMPLEXES REMARK 900 RELATED ID: 1KJH RELATED DB: PDB REMARK 900 SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION REMARK 900 FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE REMARK 900 COMPLEXES DBREF 1KJ4 A 1 99 UNP P03369 POL_HV1A2 57 155 DBREF 1KJ4 B 1 99 UNP P03369 POL_HV1A2 57 155 DBREF 1KJ4 C 1 99 UNP P03369 POL_HV1A2 57 155 DBREF 1KJ4 D 1 99 UNP P03369 POL_HV1A2 57 155 DBREF 1KJ4 P 1 10 UNP P20875 POL_HV1JR 127 136 DBREF 1KJ4 S 1 10 UNP P20875 POL_HV1JR 127 136 SEQADV 1KJ4 LYS A 7 UNP P03369 GLN 63 ENGINEERED MUTATION SEQADV 1KJ4 ASN A 25 UNP P03369 ASP 81 ENGINEERED MUTATION SEQADV 1KJ4 LYS B 7 UNP P03369 GLN 63 ENGINEERED MUTATION SEQADV 1KJ4 ASN B 25 UNP P03369 ASP 81 ENGINEERED MUTATION SEQADV 1KJ4 LYS C 7 UNP P03369 GLN 63 ENGINEERED MUTATION SEQADV 1KJ4 ASN C 25 UNP P03369 ASP 81 ENGINEERED MUTATION SEQADV 1KJ4 LYS D 7 UNP P03369 GLN 63 ENGINEERED MUTATION SEQADV 1KJ4 ASN D 25 UNP P03369 ASP 81 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN 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 GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL 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 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN 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 GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL 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 SEQRES 1 C 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 C 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 C 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO SEQRES 4 C 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 C 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 6 C 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 C 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 C 99 GLN ILE GLY CYS THR LEU ASN PHE SEQRES 1 D 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 D 99 ARG ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 D 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET ASN LEU PRO SEQRES 4 D 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 D 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE PRO VAL GLU SEQRES 6 D 99 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 D 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 D 99 GLN ILE GLY CYS THR LEU ASN PHE SEQRES 1 P 10 VAL SER GLN ASN TYR PRO ILE VAL GLN ASN SEQRES 1 S 10 VAL SER GLN ASN TYR PRO ILE VAL GLN ASN HET ACT A 504 4 HET ACT A 506 4 HET ACT A 512 4 HET ACT A 521 4 HET ACT B 501 4 HET ACT B 502 4 HET ACT B 522 4 HET ACT C 516 4 HET ACT C 524 4 HET ACT D 511 4 HET ACT D 518 4 HET ACT D 523 4 HETNAM ACT ACETATE ION FORMUL 7 ACT 12(C2 H3 O2 1-) FORMUL 19 HOH *43(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 ILE B 93 1 8 HELIX 3 3 GLY C 86 THR C 91 1 6 HELIX 4 4 GLY D 86 THR D 91 1 6 HELIX 5 5 GLN D 92 GLY D 94 5 3 SHEET 1 A 4 GLN A 2 THR A 4 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 THR A 96 O ASN B 98 SHEET 4 A 4 GLN B 2 THR B 4 -1 O ILE B 3 N LEU A 97 SHEET 1 B 3 LEU A 10 ILE A 15 0 SHEET 2 B 3 GLN A 18 LEU A 24 -1 O ALA A 22 N VAL A 11 SHEET 3 B 3 ILE A 84 ILE A 85 1 O ILE A 85 N LEU A 23 SHEET 1 C 5 THR A 31 LEU A 33 0 SHEET 2 C 5 LYS A 70 VAL A 77 1 O LEU A 76 N THR A 31 SHEET 3 C 5 PHE A 53 GLU A 65 -1 N VAL A 64 O ALA A 71 SHEET 4 C 5 LYS A 43 GLY A 48 -1 N LYS A 45 O VAL A 56 SHEET 5 C 5 SER P 2 GLN P 3 1 O SER P 2 N GLY A 48 SHEET 1 D 3 LEU B 10 ILE B 15 0 SHEET 2 D 3 GLN B 18 LEU B 24 -1 O ALA B 22 N VAL B 11 SHEET 3 D 3 ILE B 84 ILE B 85 1 O ILE B 85 N LEU B 23 SHEET 1 E 5 THR B 31 GLU B 34 0 SHEET 2 E 5 HIS B 69 GLY B 78 1 O LEU B 76 N THR B 31 SHEET 3 E 5 GLY B 52 ILE B 66 -1 N ILE B 66 O HIS B 69 SHEET 4 E 5 LYS B 43 GLY B 49 -1 N LYS B 45 O VAL B 56 SHEET 5 E 5 ILE P 7 VAL P 8 -1 O VAL P 8 N GLY B 48 SHEET 1 F 4 GLN C 2 THR C 4 0 SHEET 2 F 4 THR D 96 ASN D 98 -1 O LEU D 97 N ILE C 3 SHEET 3 F 4 THR C 96 ASN C 98 -1 N THR C 96 O ASN D 98 SHEET 4 F 4 GLN D 2 THR D 4 -1 O ILE D 3 N LEU C 97 SHEET 1 G 6 VAL C 32 LEU C 33 0 SHEET 2 G 6 HIS C 69 VAL C 77 1 O LEU C 76 N LEU C 33 SHEET 3 G 6 GLY C 52 ILE C 66 -1 N ILE C 62 O GLY C 73 SHEET 4 G 6 LEU C 10 ILE C 15 -1 N ARG C 14 O GLU C 65 SHEET 5 G 6 LEU C 19 LEU C 24 -1 O ALA C 22 N VAL C 11 SHEET 6 G 6 ILE C 84 ILE C 85 1 O ILE C 85 N LEU C 23 SHEET 1 H 5 VAL C 32 LEU C 33 0 SHEET 2 H 5 HIS C 69 VAL C 77 1 O LEU C 76 N LEU C 33 SHEET 3 H 5 GLY C 52 ILE C 66 -1 N ILE C 62 O GLY C 73 SHEET 4 H 5 PRO C 44 GLY C 49 -1 N LYS C 45 O VAL C 56 SHEET 5 H 5 GLN S 3 ASN S 4 1 O ASN S 4 N GLY C 48 SHEET 1 I 3 LEU D 10 ILE D 15 0 SHEET 2 I 3 GLN D 18 LEU D 24 -1 O LYS D 20 N ILE D 13 SHEET 3 I 3 ILE D 84 ILE D 85 1 O ILE D 85 N LEU D 23 SHEET 1 J 4 VAL D 32 LEU D 33 0 SHEET 2 J 4 HIS D 69 VAL D 77 1 O LEU D 76 N LEU D 33 SHEET 3 J 4 GLY D 52 ILE D 66 -1 N VAL D 64 O ALA D 71 SHEET 4 J 4 LYS D 43 GLY D 49 -1 N LYS D 43 O GLN D 58 SITE 1 AC1 1 HIS B 69 SITE 1 AC2 2 TRP B 6 LYS B 7 SITE 1 AC3 2 LYS A 7 ARG A 8 SITE 1 AC4 3 GLY A 73 THR A 74 ASN A 88 SITE 1 AC5 2 ARG A 14 HIS D 69 SITE 1 AC6 5 GLY B 17 GLY C 73 THR C 74 ASN C 88 SITE 2 AC6 5 GLN C 92 SITE 1 AC7 2 ARG D 14 GLY D 17 SITE 1 AC8 3 ARG B 8 ARG D 8 LEU D 10 SITE 1 AC9 3 ACT C 524 ARG D 8 VAL S 1 SITE 1 BC1 3 ARG C 87 TRP D 6 ACT D 523 CRYST1 91.651 93.808 118.172 90.00 90.00 90.00 I 2 2 2 32 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 0.010911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008462 0.00000