PDB Short entry for 1MS6 HEADER HYDROLASE 19-SEP-02 1MS6 TITLE DIPEPTIDE NITRILE INHIBITOR BOUND TO CATHEPSIN S. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN S; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.27; COMPND 5 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, CATHEPSIN, PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.WARD,D.S.THOMSON,L.L.FRYE,C.L.CYWIN,T.MORWICK, AUTHOR 2 M.J.EMMANUEL,R.ZINDELL,D.MCNEIL,Y.BEKKALI,M.GIRADOT, AUTHOR 3 M.HRAPCHAK,M.DETURI,K.CRANE,D.WHITE,S.PAV,Y.WANG,M.H.HAO, AUTHOR 4 C.A.GRYGON,M.E.LABADIA,D.M.FREEMAN,W.DAVIDSON,J.L.HOPKINS, AUTHOR 5 M.L.BROWN,D.M.SPERO REVDAT 2 24-FEB-09 1MS6 1 VERSN REVDAT 1 22-APR-03 1MS6 0 JRNL AUTH Y.D.WARD,D.S.THOMSON,L.L.FRYE,C.L.CYWIN,T.MORWICK, JRNL AUTH 2 M.J.EMMANUEL,R.ZINDELL,D.MCNEIL,Y.BEKKALI, JRNL AUTH 3 M.GIRADOT,M.HRAPCHAK,M.DETURI,K.CRANE,D.WHITE, JRNL AUTH 4 S.PAV,Y.WANG,M.H.HAO,C.A.GRYGON,M.E.LABADIA, JRNL AUTH 5 D.M.FREEMAN,W.DAVIDSON,J.L.HOPKINS,M.L.BROWN, JRNL AUTH 6 D.M.SPERO JRNL TITL DESIGN AND SYNTHESIS OF DIPEPTIDE NITRILES AS JRNL TITL 2 REVERSIBLE AND POTENT CATHEPSIN S INHIBITORS JRNL REF J.MED.CHEM. V. 45 5471 2002 JRNL REFN ISSN 0022-2623 JRNL PMID 12459015 JRNL DOI 10.1021/JM020209I REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : 42565 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) : 0.155 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2130 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 : 1685 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 0 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) : 0.21 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.33 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.77 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 1MS6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-02. REMARK 100 THE RCSB ID CODE IS RCSB017145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277.2K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 75.03500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.51750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.55250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.03500 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 112.55250 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 37.51750 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 HIS A 218 REMARK 465 HIS A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 HIS A 222 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 THR A 58 -130.32 -107.18 REMARK 500 ASN A 163 -2.54 -149.23 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 BLN A 281 DBREF 1MS6 A 1 217 UNP P25774 CATS_HUMAN 115 331 SEQADV 1MS6 HIS A 218 UNP P25774 EXPRESSION TAG SEQADV 1MS6 HIS A 219 UNP P25774 EXPRESSION TAG SEQADV 1MS6 HIS A 220 UNP P25774 EXPRESSION TAG SEQADV 1MS6 HIS A 221 UNP P25774 EXPRESSION TAG SEQADV 1MS6 HIS A 222 UNP P25774 EXPRESSION TAG SEQRES 1 A 222 LEU PRO ASP SER VAL ASP TRP ARG GLU LYS GLY CYS VAL SEQRES 2 A 222 THR GLU VAL LYS TYR GLN GLY SER CYS GLY ALA CYS TRP SEQRES 3 A 222 ALA PHE SER ALA VAL GLY ALA LEU GLU ALA GLN LEU LYS SEQRES 4 A 222 LEU LYS THR GLY LYS LEU VAL SER LEU SER ALA GLN ASN SEQRES 5 A 222 LEU VAL ASP CYS SER THR GLU LYS TYR GLY ASN LYS GLY SEQRES 6 A 222 CYS ASN GLY GLY PHE MET THR THR ALA PHE GLN TYR ILE SEQRES 7 A 222 ILE ASP ASN LYS GLY ILE ASP SER ASP ALA SER TYR PRO SEQRES 8 A 222 TYR LYS ALA MET ASP GLN LYS CYS GLN TYR ASP SER LYS SEQRES 9 A 222 TYR ARG ALA ALA THR CYS SER LYS TYR THR GLU LEU PRO SEQRES 10 A 222 TYR GLY ARG GLU ASP VAL LEU LYS GLU ALA VAL ALA ASN SEQRES 11 A 222 LYS GLY PRO VAL SER VAL GLY VAL ASP ALA ARG HIS PRO SEQRES 12 A 222 SER PHE PHE LEU TYR ARG SER GLY VAL TYR TYR GLU PRO SEQRES 13 A 222 SER CYS THR GLN ASN VAL ASN HIS GLY VAL LEU VAL VAL SEQRES 14 A 222 GLY TYR GLY ASP LEU ASN GLY LYS GLU TYR TRP LEU VAL SEQRES 15 A 222 LYS ASN SER TRP GLY HIS ASN PHE GLY GLU GLU GLY TYR SEQRES 16 A 222 ILE ARG MET ALA ARG ASN LYS GLY ASN HIS CYS GLY ILE SEQRES 17 A 222 ALA SER PHE PRO SER TYR PRO GLU ILE HIS HIS HIS HIS SEQRES 18 A 222 HIS HET BLN A 281 29 HETNAM BLN MORPHOLINE-4-CARBOXYLIC ACID [1S-(2-BENZYLOXY-1R- HETNAM 2 BLN CYANO-ETHYLCARBAMOYL)-3-METHYL-BUTYL]AMIDE FORMUL 2 BLN C21 H30 N4 O4 HELIX 1 1 ALA A 24 GLY A 43 1 20 HELIX 2 2 SER A 49 SER A 57 1 9 HELIX 3 3 THR A 58 GLY A 62 5 5 HELIX 4 4 LYS A 64 GLY A 68 5 5 HELIX 5 5 PHE A 70 LYS A 82 1 13 HELIX 6 6 ASP A 102 LYS A 104 5 3 HELIX 7 7 ARG A 120 LYS A 131 1 12 HELIX 8 8 HIS A 142 TYR A 148 1 7 HELIX 9 9 ASN A 204 ILE A 208 5 5 SHEET 1 A 5 VAL A 152 TYR A 153 0 SHEET 2 A 5 TYR A 195 ALA A 199 1 O ARG A 197 N TYR A 153 SHEET 3 A 5 LYS A 177 LYS A 183 -1 N TRP A 180 O MET A 198 SHEET 4 A 5 HIS A 164 LEU A 174 -1 N LEU A 167 O LYS A 183 SHEET 5 A 5 VAL A 5 ASP A 6 -1 N VAL A 5 O TYR A 171 SHEET 1 B 5 VAL A 152 TYR A 153 0 SHEET 2 B 5 TYR A 195 ALA A 199 1 O ARG A 197 N TYR A 153 SHEET 3 B 5 LYS A 177 LYS A 183 -1 N TRP A 180 O MET A 198 SHEET 4 B 5 HIS A 164 LEU A 174 -1 N LEU A 167 O LYS A 183 SHEET 5 B 5 VAL A 134 VAL A 138 -1 N VAL A 134 O VAL A 168 SHEET 1 C 2 ILE A 84 ASP A 85 0 SHEET 2 C 2 ARG A 106 ALA A 108 -1 O ALA A 107 N ILE A 84 SHEET 1 D 2 LYS A 112 GLU A 115 0 SHEET 2 D 2 SER A 213 GLU A 216 -1 O TYR A 214 N THR A 114 SSBOND 1 CYS A 22 CYS A 66 1555 1555 2.04 SSBOND 2 CYS A 56 CYS A 99 1555 1555 2.03 SSBOND 3 CYS A 158 CYS A 206 1555 1555 2.04 LINK SG CYS A 25 C BLN A 281 1555 1555 3.44 LINK SG CYS A 25 C' BLN A 281 1555 1555 1.90 SITE 1 AC1 16 GLN A 19 GLY A 23 ALA A 24 CYS A 25 SITE 2 AC1 16 TRP A 26 GLY A 62 LYS A 64 ASN A 67 SITE 3 AC1 16 GLY A 68 GLY A 69 PHE A 70 ALA A 140 SITE 4 AC1 16 ARG A 141 PHE A 146 ASN A 163 TRP A 186 CRYST1 85.290 85.290 150.070 90.00 90.00 90.00 P 41 2 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 0.011725 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011725 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006664 0.00000