HEADER HYDROLASE/HYDROLASE INHIBITOR 14-AUG-10 3OF8 TITLE STRUCTURAL BASIS FOR REVERSIBLE AND IRREVERSIBLE INHIBITION OF HUMAN TITLE 2 CATHEPSIN L BY THEIR RESPECTIVE DIPEPTIDYL GLYOXAL AND TITLE 3 DIAZOMETHYLKETONE INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN L1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 113-333; COMPND 5 SYNONYM: MAJOR EXCRETED PROTEIN, MEP, CATHEPSIN L1 HEAVY CHAIN, COMPND 6 CATHEPSIN L1 LIGHT CHAIN; COMPND 7 EC: 3.4.22.15; COMPND 8 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: CTSL1, CTSL; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC9 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.T.SHENOY,J.SIVARAMAN REVDAT 5 06-SEP-23 3OF8 1 REMARK REVDAT 4 17-JUL-19 3OF8 1 REMARK LINK REVDAT 3 08-NOV-17 3OF8 1 REMARK REVDAT 2 05-JAN-11 3OF8 1 JRNL REVDAT 1 08-DEC-10 3OF8 0 JRNL AUTH R.T.SHENOY,J.SIVARAMAN JRNL TITL STRUCTURAL BASIS FOR REVERSIBLE AND IRREVERSIBLE INHIBITION JRNL TITL 2 OF HUMAN CATHEPSIN L BY THEIR RESPECTIVE DIPEPTIDYL GLYOXAL JRNL TITL 3 AND DIAZOMETHYLKETONE INHIBITORS. JRNL REF J.STRUCT.BIOL. V. 173 14 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 20850545 JRNL DOI 10.1016/J.JSB.2010.09.007 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 10120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 485 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.6670 - 3.1730 1.00 3422 177 0.1920 0.2398 REMARK 3 2 3.1730 - 2.5186 1.00 3347 168 0.1840 0.2525 REMARK 3 3 2.5186 - 2.2000 0.85 2866 140 0.2142 0.3012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 40.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.700 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) : -4.53430 REMARK 3 B22 (A**2) : -4.53430 REMARK 3 B33 (A**2) : 9.06850 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1793 REMARK 3 ANGLE : 1.206 2420 REMARK 3 CHIRALITY : 0.074 238 REMARK 3 PLANARITY : 0.009 322 REMARK 3 DIHEDRAL : 18.195 649 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3OF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1CS8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM ACETATE PH 5.1, 100 MM REMARK 280 NACL, AND 1MM EDTA, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K, PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.34533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.67267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.00900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.33633 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.68167 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLU A 1 CA REMARK 480 ASN A 109 CG OD1 REMARK 480 GLN A 119 CD REMARK 480 ASP A 156 CG REMARK 480 GLU A 177 CA REMARK 480 GLU A 192 CD OE1 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 ALA A 2 148.89 76.75 REMARK 500 SER A 58 30.03 -94.77 REMARK 500 LYS A 148 -44.04 -133.65 REMARK 500 THR A 176 -85.43 -52.73 REMARK 500 ASP A 179 -59.11 -154.77 REMARK 500 ALA A 215 52.20 -148.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR Z-PHE-TYR (OBUT)-COCHO IS AN ALDEHYDE. AS IT GETS REMARK 600 COVALENTLY ATTACHED TO THE CYS25 THIOL GROUP, IT FORMS A REMARK 600 THIOHEMIACETAL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE ENZYME INHIBITOR REMARK 630 MOLECULE NAME: NALPHA-[(BENZYLOXY)CARBONYL]-N-[(2S)-1-(4-TERT- REMARK 630 BUTOXYPHENYL)-4-HYDROXY-3-OXOBUTAN-2-YL]-L-PHENYLALANINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 I0Y A 501 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ PHE TY0 REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I0Y A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OF9 RELATED DB: PDB DBREF 3OF8 A 1 221 UNP P07711 CATL1_HUMAN 113 333 SEQRES 1 A 221 GLU ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR SEQRES 2 A 221 VAL THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS SEQRES 3 A 221 TRP ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET SEQRES 4 A 221 PHE ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN SEQRES 5 A 221 ASN LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY SEQRES 6 A 221 CYS ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL SEQRES 7 A 221 GLN ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO SEQRES 8 A 221 TYR GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS SEQRES 9 A 221 TYR SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO SEQRES 10 A 221 LYS GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL SEQRES 11 A 221 GLY PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER SEQRES 12 A 221 PHE LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP SEQRES 13 A 221 CYS SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL SEQRES 14 A 221 GLY TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS SEQRES 15 A 221 TYR TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY SEQRES 16 A 221 MET GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN SEQRES 17 A 221 HIS CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL HET I0Y A 501 39 HETNAM I0Y NALPHA-[(BENZYLOXY)CARBONYL]-N-[(2S)-1-(4-TERT- HETNAM 2 I0Y BUTOXYPHENYL)-4-HYDROXY-3-OXOBUTAN-2-YL]-L- HETNAM 3 I0Y PHENYLALANINAMIDE HETSYN I0Y Z-PHE-TYR(OBUT)-COCHO FORMUL 2 I0Y C31 H36 N2 O6 FORMUL 3 HOH *47(H2 O) HELIX 1 1 ARG A 9 GLY A 12 5 4 HELIX 2 2 SER A 25 GLY A 44 1 20 HELIX 3 3 SER A 50 SER A 58 1 9 HELIX 4 4 GLY A 59 GLY A 62 5 4 HELIX 5 5 GLU A 64 GLY A 68 5 5 HELIX 6 6 LEU A 70 GLY A 82 1 13 HELIX 7 7 ASN A 102 LYS A 104 5 3 HELIX 8 8 GLN A 119 VAL A 130 1 12 HELIX 9 9 HIS A 141 PHE A 146 1 6 HELIX 10 10 ASN A 208 ILE A 212 5 5 SHEET 1 A 3 VAL A 6 ASP A 7 0 SHEET 2 A 3 HIS A 164 PHE A 173 -1 O TYR A 171 N VAL A 6 SHEET 3 A 3 ILE A 133 ILE A 137 -1 N VAL A 135 O VAL A 166 SHEET 1 B 5 VAL A 6 ASP A 7 0 SHEET 2 B 5 HIS A 164 PHE A 173 -1 O TYR A 171 N VAL A 6 SHEET 3 B 5 LYS A 182 LYS A 187 -1 O LYS A 187 N LEU A 167 SHEET 4 B 5 TYR A 199 ALA A 203 -1 O VAL A 200 N VAL A 186 SHEET 5 B 5 ILE A 151 TYR A 152 1 N TYR A 152 O LYS A 201 SHEET 1 C 2 LEU A 84 ASP A 85 0 SHEET 2 C 2 SER A 106 ALA A 108 -1 O VAL A 107 N LEU A 84 SHEET 1 D 2 GLY A 112 ASP A 115 0 SHEET 2 D 2 SER A 217 THR A 220 -1 O THR A 220 N GLY A 112 SSBOND 1 CYS A 23 CYS A 66 1555 1555 2.05 SSBOND 2 CYS A 57 CYS A 99 1555 1555 2.04 SSBOND 3 CYS A 157 CYS A 210 1555 1555 2.04 LINK SG CYS A 26 C21 I0Y A 501 1555 1555 1.83 SITE 1 AC1 16 ARG A 9 GLU A 10 GLN A 20 CYS A 26 SITE 2 AC1 16 TRP A 27 GLY A 62 GLU A 64 GLY A 68 SITE 3 AC1 16 GLY A 69 LEU A 70 MET A 71 ALA A 136 SITE 4 AC1 16 ASP A 163 HIS A 164 TRP A 190 GLU A 192 CRYST1 85.318 85.318 50.018 90.00 90.00 120.00 P 65 6 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 0.011721 0.006767 0.000000 0.00000 SCALE2 0.000000 0.013534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019993 0.00000