HEADER HYDROLASE 30-NOV-05 2F7D TITLE A MUTANT RABBIT CATHEPSIN K WITH A NITRILE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OC-2 PROTEIN; COMPND 5 EC: 3.4.22.38; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 GENE: CTSK; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS PAPAIN CYSTEINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.SOMOZA REVDAT 5 20-OCT-21 2F7D 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2F7D 1 REMARK REVDAT 3 24-FEB-09 2F7D 1 VERSN REVDAT 2 23-SEP-08 2F7D 1 JRNL REVDAT 1 07-MAR-06 2F7D 0 JRNL AUTH S.N.CRANE,W.C.BLACK,J.T.PALMER,D.E.DAVIS,E.SETTI, JRNL AUTH 2 J.ROBICHAUD,J.PAQUET,R.M.OBALLA,C.I.BAYLY,D.J.MCKAY, JRNL AUTH 3 J.R.SOMOZA,N.CHAURET,C.SETO,J.SCHEIGETZ,G.WESOLOWSKI, JRNL AUTH 4 F.MASSE,S.DESMARAIS,M.OUELLET JRNL TITL BETA-SUBSTITUTED CYCLOHEXANECARBOXAMIDE: A NONPEPTIDIC JRNL TITL 2 FRAMEWORK FOR THE DESIGN OF POTENT INHIBITORS OF CATHEPSIN JRNL TITL 3 K. JRNL REF J.MED.CHEM. V. 49 1066 2006 JRNL REFN ISSN 0022-2623 JRNL PMID 16451072 JRNL DOI 10.1021/JM051059P REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 16224 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) : 0.174 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1614 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 230 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1651 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.35600 REMARK 3 B22 (A**2) : -0.98400 REMARK 3 B33 (A**2) : -0.37200 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.193 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : MSI_CNX_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NON.PARAM REMARK 3 PARAMETER FILE 3 : MSI_CNX_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : MSI_CNX_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2F7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 3.9 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16445 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08100 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28400 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.18 M MAGNESIUM FORMATE, PH 3.9, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 19.06250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.12250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.12250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.06250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.57500 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 300 REMARK: THE CATHEPSIN K MONOMER IS PROBABLY THE BIOLOGICAL UNIT. 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 41 CD CE NZ REMARK 480 LYS A 44 CD CE NZ REMARK 480 ARG A 111 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 119 CD CE NZ REMARK 480 ARG A 127 CG CD NE CZ REMARK 480 GLN A 142 CD OE1 NE2 REMARK 480 GLU A 179 CD OE1 OE2 REMARK 480 LYS A 184 CD CE NZ 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 58.52 -95.45 REMARK 500 TYR A 86 71.80 -160.59 REMARK 500 LYS A 193 56.22 -115.42 REMARK 500 LEU A 205 58.74 -147.37 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 NOQ A 600 DBREF 2F7D A 1 211 UNP P43236 CATK_RABIT 115 329 SEQADV 2F7D ASP A 61 UNP P43236 TYR 175 ENGINEERED MUTATION SEQADV 2F7D LEU A 157 UNP P43236 VAL 274 ENGINEERED MUTATION SEQRES 1 A 215 THR PRO ASP SER ILE 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 ARG ASN SEQRES 7 A 215 ARG GLY ILE ASP SER GLU ASP ALA TYR PRO TYR VAL GLY SEQRES 8 A 215 GLN ASP 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 ASN CYS SER 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 SER 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 NOQ A 600 24 HETNAM NOQ (1R,2R)-N-(2-AMINOETHYL)-2-{[(4-METHOXYPHENYL) HETNAM 2 NOQ SULFONYL]METHYL}CYCLOHEXANECARBOXAMIDE FORMUL 2 NOQ C17 H26 N2 O4 S FORMUL 3 HOH *97(H2 O) HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 SER A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 VAL A 57 1 9 HELIX 4 4 ASP A 61 GLY A 65 5 5 HELIX 5 5 TYR A 67 ARG A 78A 1 13 HELIX 6 6 GLU A 83 TYR A 86 5 4 HELIX 7 7 ASN A 98 THR A 100 5 3 HELIX 8 8 ASN A 117 VAL A 127A 1 12 HELIX 9 9 LEU A 138 PHE A 143 1 6 HELIX 10 10 ASN A 198 ILE A 202 5 5 SHEET 1 A 3 ILE A 5 ASP A 6 0 SHEET 2 A 3 HIS A 159 GLN A 168A-1 O TYR A 166 N ILE A 5 SHEET 3 A 3 VAL A 130 ILE A 134 -1 N VAL A 130 O ALA A 163 SHEET 1 B 5 ILE A 5 ASP A 6 0 SHEET 2 B 5 HIS A 159 GLN A 168A-1 O TYR A 166 N ILE A 5 SHEET 3 B 5 ASN A 168D LYS A 174 -1 O LYS A 174 N LEU A 162 SHEET 4 B 5 TYR A 186 ALA A 190 -1 O ILE A 187 N ILE A 173 SHEET 5 B 5 VAL A 148 TYR A 149 1 N TYR A 149 O LEU A 188 SHEET 1 C 2 ILE A 80 ASP A 81 0 SHEET 2 C 2 LYS A 102 ALA A 105 -1 O ALA A 103 N ILE A 80 SHEET 1 D 2 TYR A 110 GLU A 112 0 SHEET 2 D 2 SER A 207 PRO A 209 -1 O PHE A 208 N ARG A 111 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.03 LINK SG CYS A 25 C20 NOQ A 600 1555 1555 1.75 SITE 1 AC1 10 SER A 4 GLN A 19 GLY A 23 CYS A 25 SITE 2 AC1 10 GLU A 59 ASN A 60 GLY A 65 GLY A 66 SITE 3 AC1 10 TYR A 67 ASN A 158 CRYST1 38.125 51.150 104.245 90.00 90.00 90.00 P 21 21 21 4 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 0.026230 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009593 0.00000