HEADER HYDROLASE 13-AUG-03 1Q6K TITLE CATHEPSIN K COMPLEXED WITH T-BUTYL(1S)-1-CYCLOHEXYL-2- TITLE 2 OXOETHYLCARBAMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CATHEPSIN O, CATHEPSIN X, CATHEPSIN O2; COMPND 5 EC: 3.4.22.38; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CTSK OR CTSO; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PFASTBAC KEYWDS CATHEPSIN K, CATK, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.G.CATALANO,D.N.DEATON,E.S.FURFINE,A.M.HASSELL,R.B.MCFADYEN, AUTHOR 2 A.B.MILLER,L.R.MILLER,L.M.SHEWCHUK,D.H.WILLARD,L.L.WRIGHT REVDAT 6 30-OCT-24 1Q6K 1 REMARK REVDAT 5 16-AUG-23 1Q6K 1 REMARK LINK REVDAT 4 14-FEB-18 1Q6K 1 REMARK REVDAT 3 11-OCT-17 1Q6K 1 REMARK REVDAT 2 24-FEB-09 1Q6K 1 VERSN REVDAT 1 16-MAR-04 1Q6K 0 JRNL AUTH J.G.CATALANO,D.N.DEATON,E.S.FURFINE,A.M.HASSELL, JRNL AUTH 2 R.B.MCFADYEN,A.B.MILLER,L.R.MILLER,L.M.SHEWCHUK,D.H.WILLARD, JRNL AUTH 3 L.L.WRIGHT JRNL TITL EXPLORATION OF THE P1 SAR OF ALDEHYDE CATHEPSIN K INHIBITORS JRNL REF BIOORG.MED.CHEM.LETT. V. 14 275 2004 JRNL REFN ISSN 0960-894X JRNL PMID 14684342 JRNL DOI 10.1016/J.BMCL.2003.09.088 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 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 : 12445 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) : 0.200 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 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 : 1649 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 142 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : NULL 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: NULL REMARK 4 REMARK 4 1Q6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000019979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12445 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: X-PLOR REMARK 200 STARTING MODEL: 1ATK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30% PEG8000, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 65.10600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.22150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.22150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.65900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.22150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.22150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.55300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.22150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.22150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.65900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.22150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.22150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.55300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.10600 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 SER A 4 149.62 -173.04 REMARK 500 SER A 146 -34.26 -140.06 REMARK 500 GLN A 172 -64.71 -109.38 REMARK 500 LYS A 200 54.17 -111.63 REMARK 500 LEU A 209 54.13 -147.27 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 SO4 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TCO A 0 DBREF 1Q6K A 1 215 UNP P43235 CATK_HUMAN 115 329 SEQRES 1 A 215 ALA PRO ASP SER VAL ASP TYR ARG LYS LYS GLY TYR VAL SEQRES 2 A 215 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 215 ALA PHE SER SER VAL GLY ALA LEU GLU GLY GLN LEU LYS SEQRES 4 A 215 LYS LYS THR GLY LYS LEU LEU ASN LEU SER PRO GLN ASN SEQRES 5 A 215 LEU VAL ASP CYS VAL SER GLU ASN ASP GLY CYS GLY GLY SEQRES 6 A 215 GLY TYR MET THR ASN ALA PHE GLN TYR VAL GLN LYS ASN SEQRES 7 A 215 ARG GLY ILE ASP SER GLU ASP ALA TYR PRO TYR VAL GLY SEQRES 8 A 215 GLN GLU GLU SER CYS MET TYR ASN PRO THR GLY LYS ALA SEQRES 9 A 215 ALA LYS CYS ARG GLY TYR ARG GLU ILE PRO GLU GLY ASN SEQRES 10 A 215 GLU LYS ALA LEU LYS ARG ALA VAL ALA ARG VAL GLY PRO SEQRES 11 A 215 VAL SER VAL ALA ILE ASP ALA SER LEU THR SER PHE GLN SEQRES 12 A 215 PHE TYR SER LYS GLY VAL TYR TYR ASP GLU SER CYS ASN SEQRES 13 A 215 SER ASP ASN LEU ASN HIS ALA VAL LEU ALA VAL GLY TYR SEQRES 14 A 215 GLY ILE GLN LYS GLY ASN LYS HIS TRP ILE ILE LYS ASN SEQRES 15 A 215 SER TRP GLY GLU ASN TRP GLY ASN LYS GLY TYR ILE LEU SEQRES 16 A 215 MET ALA ARG ASN LYS ASN ASN ALA CYS GLY ILE ALA ASN SEQRES 17 A 215 LEU ALA SER PHE PRO LYS MET HET SO4 A 600 5 HET TCO A 0 21 HETNAM SO4 SULFATE ION HETNAM TCO TERT-BUTYL(1S)-1-CYCLOHEXYL-2-OXOETHYLCARBAMATE FORMUL 2 SO4 O4 S 2- FORMUL 3 TCO C13 H23 N O3 FORMUL 4 HOH *142(H2 O) HELIX 1 1 SER A 24 GLY A 43 1 20 HELIX 2 2 SER A 49 VAL A 57 1 9 HELIX 3 3 ASP A 61 GLY A 65 5 5 HELIX 4 4 TYR A 67 ASN A 78 1 12 HELIX 5 5 ASN A 99 THR A 101 5 3 HELIX 6 6 ASN A 117 VAL A 128 1 12 HELIX 7 7 LEU A 139 PHE A 144 1 6 HELIX 8 8 ASN A 202 ILE A 206 5 5 SHEET 1 A 3 VAL A 5 ASP A 6 0 SHEET 2 A 3 HIS A 162 ILE A 171 -1 O TYR A 169 N VAL A 5 SHEET 3 A 3 VAL A 131 ILE A 135 -1 N VAL A 133 O VAL A 164 SHEET 1 B 5 VAL A 5 ASP A 6 0 SHEET 2 B 5 HIS A 162 ILE A 171 -1 O TYR A 169 N VAL A 5 SHEET 3 B 5 LYS A 176 LYS A 181 -1 O LYS A 181 N LEU A 165 SHEET 4 B 5 TYR A 193 ALA A 197 -1 O ILE A 194 N ILE A 180 SHEET 5 B 5 VAL A 149 TYR A 150 1 N TYR A 150 O LEU A 195 SHEET 1 C 2 ILE A 81 ASP A 82 0 SHEET 2 C 2 LYS A 103 ALA A 105 -1 O ALA A 104 N ILE A 81 SHEET 1 D 2 GLY A 109 GLU A 112 0 SHEET 2 D 2 SER A 211 LYS A 214 -1 O LYS A 214 N GLY A 109 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.04 SSBOND 2 CYS A 56 CYS A 96 1555 1555 2.03 SSBOND 3 CYS A 155 CYS A 204 1555 1555 2.03 LINK C TCO A 0 SG CYS A 25 1555 1555 2.63 SITE 1 AC1 10 ASN A 18 ARG A 108 ARG A 111 GLY A 185 SITE 2 AC1 10 GLU A 186 ASN A 187 LYS A 214 HOH A 316 SITE 3 AC1 10 HOH A 320 HOH A 342 SITE 1 AC2 10 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC2 10 LYS A 44 GLY A 64 GLY A 65 GLY A 66 SITE 3 AC2 10 LEU A 160 ASN A 161 CRYST1 56.443 56.443 130.212 90.00 90.00 90.00 P 43 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 0.017717 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007680 0.00000