HEADER HYDROLASE 30-SEP-04 1XL2
TITLE HIV-1 PROTEASE IN COMPLEX WITH PYRROLIDINMETHANAMINE
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
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 3 ORGANISM_TAXID: 11676;
SOURCE 4 GENE: GAG-POL;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P566
KEYWDS ASPARTYL PROTEASE; HIV PROTEASE; PYRROLIDINE INHIBITOR, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.BOETTCHER,E.SPECKER,A.HEINE,G.KLEBE
REVDAT 5 23-AUG-23 1XL2 1 REMARK
REVDAT 4 11-OCT-17 1XL2 1 REMARK
REVDAT 3 13-JUL-11 1XL2 1 VERSN
REVDAT 2 24-FEB-09 1XL2 1 VERSN
REVDAT 1 07-JUN-05 1XL2 0
JRNL AUTH E.SPECKER,J.BOETTCHER,H.LILIE,A.HEINE,A.SCHOOP,G.MULLER,
JRNL AUTH 2 N.GRIEBENOW,G.KLEBE
JRNL TITL AN OLD TARGET REVISITED: TWO NEW PRIVILEGED SKELETONS AND AN
JRNL TITL 2 UNEXPECTED BINDING MODE FOR HIV-PROTEASE INHIBITORS
JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 44 3140 2005
JRNL REFN ISSN 1433-7851
JRNL PMID 15822136
JRNL DOI 10.1002/ANIE.200462643
REMARK 2
REMARK 2 RESOLUTION. 1.50 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) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6
REMARK 3 CROSS-VALIDATION METHOD : FREE R
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.184
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.194
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1390
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 28064
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.169
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.179
REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.226
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1124
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 22679
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1516
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 49
REMARK 3 SOLVENT ATOMS : 190
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1755.0
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1604.0
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7111
REMARK 3 NUMBER OF RESTRAINTS : 6506
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 ANGLE DISTANCES (A) : 0.027
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.049
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.059
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.012
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.067
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE
REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
REMARK 4
REMARK 4 1XL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-04.
REMARK 100 THE DEPOSITION ID IS D_1000030477.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-MAY-04
REMARK 200 TEMPERATURE (KELVIN) : 103
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : SILICON MIRRORS, DOUBLE SILICON
REMARK 200 CRYSTAL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29849
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06300
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53
REMARK 200 COMPLETENESS FOR SHELL (%) : 77.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.00
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.54000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: 1B6N
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 33.90
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, BIS-TRIS, PH 6.5, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
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 25.95000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.10000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.85000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.10000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.95000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.85000
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: 5090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9500 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 ANGLES
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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
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 ATM2 ATM3
REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 ARG B 57 CD - NE - CZ ANGL. DEV. = 12.8 DEGREES
REMARK 500 ARG B 57 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 TYR B 59 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES
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 CL A 2601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 2602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 189 A 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 2502
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HVI RELATED DB: PDB
REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH C(2) SYMMETRY-BASED-INHIBITOR
REMARK 900 RELATED ID: 1AJX RELATED DB: PDB
REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH CYCLIC SULFONAMIDE
REMARK 900 RELATED ID: 1XL5 RELATED DB: PDB
DBREF 1XL2 A 1 99 UNP P03367 POL_HV1BR 69 167
DBREF 1XL2 B 1 99 UNP P03367 POL_HV1BR 69 167
SEQRES 1 A 99 PRO GLN ILE THR LEU TRP GLN 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 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 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 GLN 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 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 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 CL A2601 1
HET 189 A1001 41
HET CL B2602 1
HET GOL B2502 6
HETNAM CL CHLORIDE ION
HETNAM 189 N-BENZYL-2-(2,6-DIMETHYLPHENOXY)-N-[((3R,4S)-4-
HETNAM 2 189 {[ISOBUTYL(PHENYLSULFONYL)AMINO]METHYL}PYRROLIDIN-3-
HETNAM 3 189 YL)METHYL]ACETAMIDE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 CL 2(CL 1-)
FORMUL 4 189 C33 H43 N3 O4 S
FORMUL 6 GOL C3 H8 O3
FORMUL 7 HOH *190(H2 O)
HELIX 1 1 GLY A 86 THR A 91 1 6
HELIX 2 2 GLY B 86 THR B 91 1 6
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 GLN A 58 N LYS A 43
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 VAL B 75 N TYR B 59
SHEET 4 C 8 THR B 31 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 ILE B 13 O LYS B 20
SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14
SITE 1 AC1 4 GLY A 73 THR A 74 ASN A 88 HOH A2627
SITE 1 AC2 4 GLY B 73 THR B 74 ASN B 88 HOH B2662
SITE 1 AC3 19 ASP A 25 GLY A 27 VAL A 32 GLY A 48
SITE 2 AC3 19 GLY A 49 ILE A 50 THR A 80 PRO A 81
SITE 3 AC3 19 VAL A 82 ILE A 84 HOH A2679 ASP B 25
SITE 4 AC3 19 GLY B 27 ALA B 28 ILE B 47 GLY B 49
SITE 5 AC3 19 ILE B 50 PRO B 81 ILE B 84
SITE 1 AC4 6 THR B 4 ARG B 8 LEU B 10 HOH B2611
SITE 2 AC4 6 HOH B2631 HOH B2657
CRYST1 51.900 57.700 62.200 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 0.019268 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017331 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016077 0.00000