HEADER HYDROLASE 11-AUG-04 1U9V TITLE CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN TITLE 2 COMPLEX WITH THE COVALENT INHIBITOR NVP-ABE854 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 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PMBAC-HC9 KEYWDS HYDROLASE, SULFHYDRYL PROTEINASE EXPDTA X-RAY DIFFRACTION AUTHOR S.W.COWAN-JACOB REVDAT 4 25-OCT-23 1U9V 1 REMARK LINK REVDAT 3 11-OCT-17 1U9V 1 REMARK REVDAT 2 24-FEB-09 1U9V 1 VERSN REVDAT 1 11-AUG-05 1U9V 0 JRNL AUTH E.ALTMANN,S.W.COWAN-JACOB,M.MISSBACH JRNL TITL NOVEL PURINE NITRILE DERIVED INHIBITORS OF THE CYSTEINE JRNL TITL 2 PROTEASE CATHEPSIN K JRNL REF J.MED.CHEM. V. 47 5833 2004 JRNL REFN ISSN 0022-2623 JRNL PMID 15537340 JRNL DOI 10.1021/JM0493111 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 11927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 563 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) : 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 : 1631 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.27 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.562 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.84 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.845 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 294 REMARK 200 PH : 8.7 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 : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR, XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12003 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 35.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.06060 REMARK 200 R SYM (I) : 0.06060 REMARK 200 FOR THE DATA SET : 48.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18240 REMARK 200 R SYM FOR SHELL (I) : 0.18240 REMARK 200 FOR SHELL : 16.60 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: PDB ENTRY 1MEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, MAGNESIUM CHLORIDE, PH REMARK 280 8.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 56.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.60000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.35000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.60000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.35000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.45000 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 56.90000 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 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 GLY A -1 REMARK 465 ARG A 0 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 41 CG CD CE NZ REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 ARG A 127 CG CD NE CZ NH1 NH2 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 GLN A 21 38.26 -95.33 REMARK 500 ARG A 79 37.80 71.17 REMARK 500 THR A 101 179.01 -57.49 REMARK 500 SER A 146 -39.85 -133.24 REMARK 500 ASN A 159 77.16 -116.47 REMARK 500 LEU A 209 57.05 -143.93 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 IHE A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MEM RELATED DB: PDB REMARK 900 RELATED ID: 1ATK RELATED DB: PDB REMARK 900 RELATED ID: 1U9W RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH THE COVALENT INHIBITOR NVP-ABI491 REMARK 900 RELATED ID: 1U9X RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH THE COVALENT INHIBITOR NVP-ABJ688 DBREF 1U9V A -1 215 UNP P43235 CATK_HUMAN 113 329 SEQRES 1 A 217 GLY ARG ALA PRO ASP SER VAL ASP TYR ARG LYS LYS GLY SEQRES 2 A 217 TYR VAL THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER SEQRES 3 A 217 CYS TRP ALA PHE SER SER VAL GLY ALA LEU GLU GLY GLN SEQRES 4 A 217 LEU LYS LYS LYS THR GLY LYS LEU LEU ASN LEU SER PRO SEQRES 5 A 217 GLN ASN LEU VAL ASP CYS VAL SER GLU ASN ASP GLY CYS SEQRES 6 A 217 GLY GLY GLY TYR MET THR ASN ALA PHE GLN TYR VAL GLN SEQRES 7 A 217 LYS ASN ARG GLY ILE ASP SER GLU ASP ALA TYR PRO TYR SEQRES 8 A 217 VAL GLY GLN GLU GLU SER CYS MET TYR ASN PRO THR GLY SEQRES 9 A 217 LYS ALA ALA LYS CYS ARG GLY TYR ARG GLU ILE PRO GLU SEQRES 10 A 217 GLY ASN GLU LYS ALA LEU LYS ARG ALA VAL ALA ARG VAL SEQRES 11 A 217 GLY PRO VAL SER VAL ALA ILE ASP ALA SER LEU THR SER SEQRES 12 A 217 PHE GLN PHE TYR SER LYS GLY VAL TYR TYR ASP GLU SER SEQRES 13 A 217 CYS ASN SER ASP ASN LEU ASN HIS ALA VAL LEU ALA VAL SEQRES 14 A 217 GLY TYR GLY ILE GLN LYS GLY ASN LYS HIS TRP ILE ILE SEQRES 15 A 217 LYS ASN SER TRP GLY GLU ASN TRP GLY ASN LYS GLY TYR SEQRES 16 A 217 ILE LEU MET ALA ARG ASN LYS ASN ASN ALA CYS GLY ILE SEQRES 17 A 217 ALA ASN LEU ALA SER PHE PRO LYS MET HET IHE A 300 27 HETNAM IHE 6-(CYCLOHEXYLAMINO)-9-[2-(4-METHYLPIPERAZIN-1-YL)- HETNAM 2 IHE ETHYL]-9H-PURINE-2-CARBONITRILE HETSYN IHE NVP-ABE854 FORMUL 2 IHE C19 H28 N8 FORMUL 3 HOH *81(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 ARG A 79 1 13 HELIX 5 5 ASN A 117 VAL A 128 1 12 HELIX 6 6 LEU A 139 PHE A 144 1 6 HELIX 7 7 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 GLN A 172 -1 O TYR A 169 N VAL A 5 SHEET 3 A 3 VAL A 131 ILE A 135 -1 N ILE A 135 O HIS A 162 SHEET 1 B 5 VAL A 5 ASP A 6 0 SHEET 2 B 5 HIS A 162 GLN A 172 -1 O TYR A 169 N VAL A 5 SHEET 3 B 5 ASN A 175 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 TYR A 110 GLU A 112 0 SHEET 2 C 2 SER A 211 PRO A 213 -1 O PHE A 212 N ARG A 111 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.05 SSBOND 2 CYS A 56 CYS A 96 1555 1555 2.29 SSBOND 3 CYS A 155 CYS A 204 1555 1555 2.29 LINK SG CYS A 25 C27 IHE A 300 1555 1555 1.77 SITE 1 AC1 14 TYR A 12 GLN A 19 GLY A 23 CYS A 25 SITE 2 AC1 14 LYS A 40 THR A 42 GLY A 43 GLY A 64 SITE 3 AC1 14 GLY A 66 TYR A 67 ALA A 134 ASN A 161 SITE 4 AC1 14 HIS A 162 HOH A 650 CRYST1 63.200 63.200 113.800 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 0.015823 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008787 0.00000