HEADER HYDROLASE 14-OCT-10 2XU1 TITLE CATHEPSIN L WITH A NITRILE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN L1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 114-333; COMPND 5 SYNONYM: MAJOR EXCRETED PROTEIN, MEP; COMPND 6 EC: 3.4.22.15; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS HYDROLASE, DRUG DESIGN, THIOL PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,J.M.BENZ,S.STEINBACHER,W.HAAP REVDAT 1 12-JAN-11 2XU1 0 JRNL AUTH L.A.HARDEGGER,B.KUHN,B.SPINNLER,L.ANSELM,R.ECABERT,M.STIHLE, JRNL AUTH 2 B.GSELL,R.THOMA,J.DIEZ,J.BENZ,J.M.PLANCHER,G.HARTMANN, JRNL AUTH 3 D.W.BANNER,W.HAAP,F.DIEDERICH JRNL TITL SYSTEMATIC INVESTIGATION OF HALOGEN BONDING IN JRNL TITL 2 PROTEIN-LIGAND INTERACTIONS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 50 314 2011 JRNL REFN ISSN 1433-7851 JRNL PMID 21184410 JRNL DOI 10.1002/ANIE.201006781 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0041 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 87.09 REMARK 3 NUMBER OF REFLECTIONS : 120732 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 + TEST SET) : 0.23504 REMARK 3 R VALUE (WORKING SET) : 0.23367 REMARK 3 FREE R VALUE : 0.27217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.6 REMARK 3 FREE R VALUE TEST SET COUNT : 4452 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.450 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.488 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7602 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.324 REMARK 3 BIN FREE R VALUE SET COUNT : 292 REMARK 3 BIN FREE R VALUE : 0.366 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6836 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 140 REMARK 3 SOLVENT ATOMS : 720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.6 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.311 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05 REMARK 3 B22 (A**2) : -0.13 REMARK 3 B33 (A**2) : -0.25 REMARK 3 B12 (A**2) : -0.10 REMARK 3 B13 (A**2) : 0.10 REMARK 3 B23 (A**2) : -0.65 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.292 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7185 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9776 ; 1.421 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 900 ; 5.611 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 343 ;38.043 ;25.102 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1121 ;13.472 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;14.929 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 965 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5674 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 46678 ; 0.016 ; 0.200 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2XU1 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-OCT-10. REMARK 100 THE PDBE ID CODE IS EBI-45767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.008 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 137183 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.45 REMARK 200 RESOLUTION RANGE LOW (A) : 50.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 2.28 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.79 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.29 REMARK 200 R MERGE FOR SHELL (I) : 0.52 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.46 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: ISOMORPHOUS TO PDB ENTRY 3HWN REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.5 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 2000, PH 4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 350 REMARK 350 BIOMOLECULE: 4 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: D 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 SER A 174 REMARK 465 THR A 175 REMARK 465 GLU A 176 REMARK 465 SER A 177 REMARK 465 ASP A 178 REMARK 465 GLU D 173 REMARK 465 SER D 174 REMARK 465 THR D 175 REMARK 465 GLU D 176 REMARK 465 SER D 177 REMARK 465 ASP D 178 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 2176 O HOH B 2197 1.80 REMARK 500 O HOH B 2019 O HOH B 2029 1.93 REMARK 500 O HOH C 2019 O HOH D 2024 1.97 REMARK 500 O HOH B 2031 O HOH B 2067 2.15 REMARK 500 O HOH A 2150 O HOH A 2152 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 2085 O HOH A 2119 1565 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 117 55.52 -68.86 REMARK 500 ARG A 205 68.45 -119.78 REMARK 500 ALA A 214 58.49 -154.54 REMARK 500 ASP B 160 46.94 -103.09 REMARK 500 ASP B 162 12.05 -140.53 REMARK 500 SER B 174 -175.08 67.87 REMARK 500 ASP B 204 37.33 70.09 REMARK 500 CYS B 209 13.10 58.33 REMARK 500 ALA B 214 57.75 -153.11 REMARK 500 LYS C 117 49.33 -82.41 REMARK 500 ASP C 162 11.84 -141.14 REMARK 500 CYS C 209 17.48 57.11 REMARK 500 GLN D 21 35.99 -92.50 REMARK 500 LYS D 117 48.15 -81.12 REMARK 500 ASP D 162 13.86 -140.23 REMARK 500 ARG D 205 63.39 -117.97 REMARK 500 CYS D 209 13.52 58.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 PROTEIN WAS CRYSTALLIZED AFTER TREATMENT WITH REMARK 600 (2S, 4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1-(4-CHLORO-PHENYL) REMARK 600 -CYCLOPROPANECARBONYL]-PYRROLIDINE-2-CARBOXYLIC ACID (1-CYANO- REMARK 600 CYCLOPROPYL)-AMIDE. LIGAND WITH RESIDUE NAME 424 DERIVES FROM THIS. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 424 A1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 424 B1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 424 C1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 424 D1221 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CJL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CYSTEINE PROTEASE REMARK 900 PROFORM REMARK 900 RELATED ID: 1CS8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PROCATHEPSIN L REMARK 900 RELATED ID: 2XU4 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 2VHS RELATED DB: PDB REMARK 900 CATHSILICATEIN, A CHIMERA REMARK 900 RELATED ID: 1ICF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED REMARK 900 P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L REMARK 900 RELATED ID: 2XU3 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 900 RELATED ID: 1MHW RELATED DB: PDB REMARK 900 DESIGN OF NON-COVALENT INHIBITORS OF HUMAN REMARK 900 CATHEPSIN L.FROM THE 96-RESIDUE PROREGION REMARK 900 TO OPTIMIZED TRIPEPTIDES REMARK 900 RELATED ID: 2XU5 RELATED DB: PDB REMARK 900 CATHEPSIN L WITH A NITRILE INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 THR110 TO ALA MUTANT (T110A) CORRESPONDING TO RESIDUE 223 REMARK 999 IN THE UNIPROT NUMBERING. DBREF 2XU1 A 1 220 UNP P07711 CATL1_HUMAN 114 333 DBREF 2XU1 B 1 220 UNP P07711 CATL1_HUMAN 114 333 DBREF 2XU1 C 1 220 UNP P07711 CATL1_HUMAN 114 333 DBREF 2XU1 D 1 220 UNP P07711 CATL1_HUMAN 114 333 SEQADV 2XU1 ALA A 110 UNP P07711 THR 223 ENGINEERED MUTATION SEQADV 2XU1 ALA B 110 UNP P07711 THR 223 ENGINEERED MUTATION SEQADV 2XU1 ALA C 110 UNP P07711 THR 223 ENGINEERED MUTATION SEQADV 2XU1 ALA D 110 UNP P07711 THR 223 ENGINEERED MUTATION SEQRES 1 A 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 A 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 A 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 A 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 A 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 A 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 A 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 A 220 SER VAL ALA ASN ASP ALA GLY PHE VAL ASP ILE PRO LYS SEQRES 10 A 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 A 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 A 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 A 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 A 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 A 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 A 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 A 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL SEQRES 1 B 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 B 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 B 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 B 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 B 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 B 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 B 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 B 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 B 220 SER VAL ALA ASN ASP ALA GLY PHE VAL ASP ILE PRO LYS SEQRES 10 B 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 B 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 B 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 B 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 B 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 B 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 B 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 B 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL SEQRES 1 C 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 C 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 C 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 C 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 C 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 C 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 C 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 C 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 C 220 SER VAL ALA ASN ASP ALA GLY PHE VAL ASP ILE PRO LYS SEQRES 10 C 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 C 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 C 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 C 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 C 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 C 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 C 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 C 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL SEQRES 1 D 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 D 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 D 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 D 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 D 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 D 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 D 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 D 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 D 220 SER VAL ALA ASN ASP ALA GLY PHE VAL ASP ILE PRO LYS SEQRES 10 D 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 D 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 D 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 D 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 D 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 D 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 D 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 D 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL HET 424 A1221 35 HET 424 B1221 35 HET 424 C1221 35 HET 424 D1221 35 HETNAM 424 (2S,4R)-1-[1-(4-CHLOROPHENYL)CYCLOPROPYL]CARBONYL HETNAM 2 424 -4-(2-CHLOROPHENYL)SULFONYL-N-[1-(IMINOMETHYL) HETNAM 3 424 CYCLOPROPYL]PYRROLIDINE-2-CARBOXAMIDE FORMUL 5 424 4(C25 H25 CL2 N3 O4 S) FORMUL 6 HOH *720(H2 O) HELIX 1 1 SER A 24 GLY A 43 1 20 HELIX 2 2 SER A 49 SER A 57 1 9 HELIX 3 3 GLY A 58 GLY A 61 5 4 HELIX 4 4 GLU A 63 GLY A 67 5 5 HELIX 5 5 LEU A 69 GLY A 81 1 13 HELIX 6 6 ASN A 101 LYS A 103 5 3 HELIX 7 7 GLN A 118 VAL A 129 1 12 HELIX 8 8 HIS A 140 PHE A 145 1 6 HELIX 9 9 ASN A 207 ILE A 211 5 5 HELIX 10 10 ARG B 8 GLY B 11 5 4 HELIX 11 11 SER B 24 GLY B 43 1 20 HELIX 12 12 SER B 49 SER B 57 1 9 HELIX 13 13 GLY B 58 GLY B 61 5 4 HELIX 14 14 GLU B 63 CYS B 65 5 3 HELIX 15 15 LEU B 69 GLY B 81 1 13 HELIX 16 16 ASN B 101 LYS B 103 5 3 HELIX 17 17 GLN B 118 VAL B 129 1 12 HELIX 18 18 HIS B 140 PHE B 145 1 6 HELIX 19 19 THR B 175 ASN B 179 5 5 HELIX 20 20 ASN B 207 ILE B 211 5 5 HELIX 21 21 ARG C 8 GLY C 11 5 4 HELIX 22 22 SER C 24 GLY C 43 1 20 HELIX 23 23 SER C 49 SER C 57 1 9 HELIX 24 24 GLY C 58 GLY C 61 5 4 HELIX 25 25 GLU C 63 CYS C 65 5 3 HELIX 26 26 LEU C 69 GLY C 81 1 13 HELIX 27 27 ASN C 101 LYS C 103 5 3 HELIX 28 28 GLN C 118 GLY C 130 1 13 HELIX 29 29 HIS C 140 TYR C 146 1 7 HELIX 30 30 ASN C 207 ILE C 211 5 5 HELIX 31 31 SER D 24 GLY D 43 1 20 HELIX 32 32 SER D 49 SER D 57 1 9 HELIX 33 33 GLY D 58 GLY D 61 5 4 HELIX 34 34 GLU D 63 CYS D 65 5 3 HELIX 35 35 LEU D 69 GLY D 81 1 13 HELIX 36 36 ASN D 101 LYS D 103 5 3 HELIX 37 37 GLN D 118 VAL D 129 1 12 HELIX 38 38 HIS D 140 TYR D 146 1 7 HELIX 39 39 ASN D 207 ILE D 211 5 5 SHEET 1 AA 2 VAL A 5 ASP A 6 0 SHEET 2 AA 2 HIS A 163 GLY A 171 1 O TYR A 170 N VAL A 5 SHEET 1 AB 2 ILE A 132 ILE A 136 0 SHEET 2 AB 2 HIS A 163 GLY A 171 -1 O HIS A 163 N ILE A 136 SHEET 1 AC 5 ILE A 150 TYR A 151 0 SHEET 2 AC 5 TYR A 198 ALA A 202 1 O LYS A 200 N TYR A 151 SHEET 3 AC 5 TYR A 182 LYS A 186 -1 O TRP A 183 N MET A 201 SHEET 4 AC 5 HIS A 163 GLY A 171 -1 O LEU A 166 N LYS A 186 SHEET 5 AC 5 ILE A 132 ILE A 136 -1 O ILE A 132 N VAL A 167 SHEET 1 AD 5 ILE A 150 TYR A 151 0 SHEET 2 AD 5 TYR A 198 ALA A 202 1 O LYS A 200 N TYR A 151 SHEET 3 AD 5 TYR A 182 LYS A 186 -1 O TRP A 183 N MET A 201 SHEET 4 AD 5 HIS A 163 GLY A 171 -1 O LEU A 166 N LYS A 186 SHEET 5 AD 5 VAL A 5 ASP A 6 1 O VAL A 5 N TYR A 170 SHEET 1 AE 2 LEU A 83 ASP A 84 0 SHEET 2 AE 2 SER A 105 ALA A 107 -1 N VAL A 106 O LEU A 83 SHEET 1 AF 2 PHE A 112 ASP A 114 0 SHEET 2 AF 2 SER A 216 PRO A 218 -1 O TYR A 217 N VAL A 113 SHEET 1 BA 2 VAL B 5 ASP B 6 0 SHEET 2 BA 2 HIS B 163 PHE B 172 1 O TYR B 170 N VAL B 5 SHEET 1 BB 2 ILE B 132 ILE B 136 0 SHEET 2 BB 2 HIS B 163 PHE B 172 -1 O HIS B 163 N ILE B 136 SHEET 1 BC 5 ILE B 150 TYR B 151 0 SHEET 2 BC 5 TYR B 198 ALA B 202 1 O LYS B 200 N TYR B 151 SHEET 3 BC 5 LYS B 181 LYS B 186 -1 O TRP B 183 N MET B 201 SHEET 4 BC 5 HIS B 163 PHE B 172 -1 O LEU B 166 N LYS B 186 SHEET 5 BC 5 ILE B 132 ILE B 136 -1 O ILE B 132 N VAL B 167 SHEET 1 BD 5 ILE B 150 TYR B 151 0 SHEET 2 BD 5 TYR B 198 ALA B 202 1 O LYS B 200 N TYR B 151 SHEET 3 BD 5 LYS B 181 LYS B 186 -1 O TRP B 183 N MET B 201 SHEET 4 BD 5 HIS B 163 PHE B 172 -1 O LEU B 166 N LYS B 186 SHEET 5 BD 5 VAL B 5 ASP B 6 1 O VAL B 5 N TYR B 170 SHEET 1 BE 2 LEU B 83 ASP B 84 0 SHEET 2 BE 2 SER B 105 ALA B 107 -1 N VAL B 106 O LEU B 83 SHEET 1 BF 2 PHE B 112 ASP B 114 0 SHEET 2 BF 2 SER B 216 PRO B 218 -1 O TYR B 217 N VAL B 113 SHEET 1 CA 2 VAL C 5 ASP C 6 0 SHEET 2 CA 2 HIS C 163 PHE C 172 1 O TYR C 170 N VAL C 5 SHEET 1 CB 2 ILE C 132 ILE C 136 0 SHEET 2 CB 2 HIS C 163 PHE C 172 -1 O HIS C 163 N ILE C 136 SHEET 1 CC 5 ILE C 150 TYR C 151 0 SHEET 2 CC 5 TYR C 198 ALA C 202 1 O LYS C 200 N TYR C 151 SHEET 3 CC 5 LYS C 181 LYS C 186 -1 O TRP C 183 N MET C 201 SHEET 4 CC 5 HIS C 163 PHE C 172 -1 O LEU C 166 N LYS C 186 SHEET 5 CC 5 ILE C 132 ILE C 136 -1 O ILE C 132 N VAL C 167 SHEET 1 CD 5 ILE C 150 TYR C 151 0 SHEET 2 CD 5 TYR C 198 ALA C 202 1 O LYS C 200 N TYR C 151 SHEET 3 CD 5 LYS C 181 LYS C 186 -1 O TRP C 183 N MET C 201 SHEET 4 CD 5 HIS C 163 PHE C 172 -1 O LEU C 166 N LYS C 186 SHEET 5 CD 5 VAL C 5 ASP C 6 1 O VAL C 5 N TYR C 170 SHEET 1 CE 2 LEU C 83 ASP C 84 0 SHEET 2 CE 2 SER C 105 ALA C 107 -1 N VAL C 106 O LEU C 83 SHEET 1 CF 2 PHE C 112 ASP C 114 0 SHEET 2 CF 2 SER C 216 PRO C 218 -1 O TYR C 217 N VAL C 113 SHEET 1 DA 2 VAL D 5 ASP D 6 0 SHEET 2 DA 2 HIS D 163 GLY D 171 1 O TYR D 170 N VAL D 5 SHEET 1 DB 2 ILE D 132 ILE D 136 0 SHEET 2 DB 2 HIS D 163 GLY D 171 -1 O HIS D 163 N ILE D 136 SHEET 1 DC 5 ILE D 150 TYR D 151 0 SHEET 2 DC 5 TYR D 198 ALA D 202 1 O LYS D 200 N TYR D 151 SHEET 3 DC 5 TYR D 182 LYS D 186 -1 O TRP D 183 N MET D 201 SHEET 4 DC 5 HIS D 163 GLY D 171 -1 O LEU D 166 N LYS D 186 SHEET 5 DC 5 ILE D 132 ILE D 136 -1 O ILE D 132 N VAL D 167 SHEET 1 DD 5 ILE D 150 TYR D 151 0 SHEET 2 DD 5 TYR D 198 ALA D 202 1 O LYS D 200 N TYR D 151 SHEET 3 DD 5 TYR D 182 LYS D 186 -1 O TRP D 183 N MET D 201 SHEET 4 DD 5 HIS D 163 GLY D 171 -1 O LEU D 166 N LYS D 186 SHEET 5 DD 5 VAL D 5 ASP D 6 1 O VAL D 5 N TYR D 170 SHEET 1 DE 2 LEU D 83 ASP D 84 0 SHEET 2 DE 2 SER D 105 ALA D 107 -1 N VAL D 106 O LEU D 83 SHEET 1 DF 2 PHE D 112 ASP D 114 0 SHEET 2 DF 2 SER D 216 PRO D 218 -1 O TYR D 217 N VAL D 113 SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.10 SSBOND 3 CYS A 156 CYS A 209 1555 1555 2.05 SSBOND 4 CYS B 22 CYS B 65 1555 1555 2.02 SSBOND 5 CYS B 56 CYS B 98 1555 1555 2.06 SSBOND 6 CYS B 156 CYS B 209 1555 1555 2.03 SSBOND 7 CYS C 22 CYS C 65 1555 1555 2.04 SSBOND 8 CYS C 56 CYS C 98 1555 1555 2.09 SSBOND 9 CYS C 156 CYS C 209 1555 1555 2.05 SSBOND 10 CYS D 22 CYS D 65 1555 1555 2.06 SSBOND 11 CYS D 56 CYS D 98 1555 1555 2.05 SSBOND 12 CYS D 156 CYS D 209 1555 1555 2.04 LINK SG CYS A 25 C15 424 A1221 1555 1555 1.84 LINK SG CYS B 25 C15 424 B1221 1555 1555 1.86 LINK SG CYS C 25 C15 424 C1221 1555 1555 1.85 LINK SG CYS D 25 C15 424 D1221 1555 1555 1.90 SITE 1 AC1 19 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC1 19 TRP A 26 GLY A 61 GLU A 63 GLY A 67 SITE 3 AC1 19 GLY A 68 LEU A 69 MET A 70 ALA A 135 SITE 4 AC1 19 MET A 161 ASP A 162 HIS A 163 GLY A 164 SITE 5 AC1 19 ALA A 214 HOH A2094 HOH A2211 SITE 1 AC2 17 GLN B 19 GLY B 23 SER B 24 CYS B 25 SITE 2 AC2 17 TRP B 26 GLY B 61 GLY B 67 GLY B 68 SITE 3 AC2 17 LEU B 69 MET B 70 ALA B 135 MET B 161 SITE 4 AC2 17 ASP B 162 HIS B 163 GLY B 164 ALA B 214 SITE 5 AC2 17 HOH B2219 SITE 1 AC3 17 GLN C 19 GLY C 23 SER C 24 CYS C 25 SITE 2 AC3 17 TRP C 26 GLY C 61 GLY C 67 GLY C 68 SITE 3 AC3 17 LEU C 69 MET C 70 ALA C 135 MET C 161 SITE 4 AC3 17 ASP C 162 HIS C 163 GLY C 164 ALA C 214 SITE 5 AC3 17 HOH C2058 SITE 1 AC4 16 GLN D 19 GLY D 23 SER D 24 CYS D 25 SITE 2 AC4 16 TRP D 26 GLY D 61 GLY D 67 GLY D 68 SITE 3 AC4 16 LEU D 69 MET D 70 ALA D 135 MET D 161 SITE 4 AC4 16 ASP D 162 HIS D 163 GLY D 164 ALA D 214 CRYST1 57.360 62.705 68.243 105.62 93.24 115.45 P 1 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 0.017434 0.008297 0.003901 0.00000 SCALE2 0.000000 0.017662 0.006082 0.00000 SCALE3 0.000000 0.000000 0.015523 0.00000