PDB Short entry for 1AYU HEADER HYDROLASE 10-NOV-97 1AYU TITLE CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX TITLE 2 WITH A COVALENT SYMMETRIC BISCARBOHYDRAZIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.38; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: INHIBITOR COVALENTLY BOUND TO ACTIVE SITE CYS 25 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: SF21; SOURCE 6 CELL: OSTEOCLAST; SOURCE 7 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 8 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS KEYWDS HYDROLASE, SULFHYDRYL PROTEINASE EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHAO,W.W.SMITH,C.A.JANSON,S.S.ABDEL-MEGUID REVDAT 7 02-AUG-23 1AYU 1 REMARK LINK REVDAT 6 07-MAR-18 1AYU 1 REMARK REVDAT 5 29-FEB-12 1AYU 1 JRNL VERSN REVDAT 4 24-FEB-09 1AYU 1 VERSN REVDAT 3 01-APR-03 1AYU 1 JRNL REVDAT 2 13-JAN-99 1AYU 1 SOURCE COMPND REMARK FORMUL REVDAT 2 2 1 JRNL KEYWDS HEADER REVDAT 1 25-NOV-98 1AYU 0 JRNL AUTH S.K.THOMPSON,S.M.HALBERT,M.J.BOSSARD,T.A.TOMASZEK,M.A.LEVY, JRNL AUTH 2 B.ZHAO,W.W.SMITH,S.S.ABDEL-MEGUID,C.A.JANSON,K.J.D'ALESSIO, JRNL AUTH 3 M.S.MCQUENEY,B.Y.AMEGADZIE,C.R.HANNING,R.L.DESJARLAIS, JRNL AUTH 4 J.BRIAND,S.K.SARKAR,M.J.HUDDLESTON,C.F.IJAMES,S.A.CARR, JRNL AUTH 5 K.T.GARNES,A.SHU,J.R.HEYS,J.BRADBEER,D.ZEMBRYKI, JRNL AUTH 6 L.LEE-RYKACZEWSKI,I.E.JAMES,M.W.LARK,F.H.DRAKE,M.GOWEN, JRNL AUTH 7 J.G.GLEASON,D.F.VEBER JRNL TITL DESIGN OF POTENT AND SELECTIVE HUMAN CATHEPSIN K INHIBITORS JRNL TITL 2 THAT SPAN THE ACTIVE SITE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 94 14249 1997 JRNL REFN ISSN 0027-8424 JRNL PMID 9405598 JRNL DOI 10.1073/PNAS.94.26.14249 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.5 REMARK 3 NUMBER OF REFLECTIONS : 8108 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) : 0.208 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 840 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.29 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 717 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 83 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 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 : 42 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.170 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9452 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: 1ATK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% MPD, 0.1M MES, 0.1M TRIS-HCL, REMARK 280 PH7.0 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 19.16500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.16500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.65000 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: 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 TYR A 87 75.82 -162.92 REMARK 500 ALA A 105 -173.60 -176.83 REMARK 500 LYS A 106 -168.50 -165.58 REMARK 500 SER A 146 -37.58 -145.28 REMARK 500 TYR A 151 146.63 -173.82 REMARK 500 LYS A 200 61.84 -112.04 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 INA A 300 DBREF 1AYU 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 INA A 300 42 HETNAM INA 1,5-BIS(N-BENZYLOXYCARBONYL-L-LEUCINYL)CARBOHYDRAZIDE FORMUL 2 INA C29 H40 N6 O7 FORMUL 3 HOH *66(H2 O) HELIX 1 1 CYS A 25 THR A 42 1 18 HELIX 2 2 PRO A 50 CYS A 56 1 7 HELIX 3 3 GLY A 62 GLY A 64 5 3 HELIX 4 4 MET A 68 LYS A 77 1 10 HELIX 5 5 PRO A 100 GLY A 102 5 3 HELIX 6 6 GLU A 118 ARG A 127 1 10 HELIX 7 7 THR A 140 GLN A 143 1 4 HELIX 8 8 ALA A 203 GLY A 205 5 3 SHEET 1 A 2 TYR A 110 GLU A 112 0 SHEET 2 A 2 SER A 211 PRO A 213 -1 N PHE A 212 O ARG A 111 SHEET 1 B 4 VAL A 131 ILE A 135 0 SHEET 2 B 4 HIS A 162 GLN A 172 -1 N ALA A 166 O VAL A 131 SHEET 3 B 4 ASN A 175 LYS A 181 -1 N LYS A 181 O LEU A 165 SHEET 4 B 4 TYR A 193 ALA A 197 -1 N MET A 196 O TRP A 178 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 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 SG CYS A 25 C21 INA A 300 1555 1555 1.80 SITE 1 AC1 25 SER A 4 ASN A 18 GLN A 19 GLY A 20 SITE 2 AC1 25 GLN A 21 CYS A 22 GLY A 23 SER A 24 SITE 3 AC1 25 CYS A 25 TRP A 26 GLU A 59 ASP A 61 SITE 4 AC1 25 GLY A 65 GLY A 66 TYR A 67 MET A 68 SITE 5 AC1 25 PHE A 144 TYR A 145 SER A 146 LYS A 147 SITE 6 AC1 25 ASN A 161 HIS A 162 ALA A 163 ILE A 171 SITE 7 AC1 25 TRP A 184 CRYST1 38.330 51.300 103.860 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 0.026089 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009628 0.00000