PDB Short entry for 1GMY HEADER HYDROLASE/INHIBITOR 25-SEP-01 1GMY TITLE CATHEPSIN B COMPLEXED WITH DIPEPTIDYL NITRILE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN B; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: PROTEASE DOMAIN, RESIDUES 80-333; COMPND 5 EC: 3.4.22.1; COMPND 6 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: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS HYDROLASE/INHIBITOR, COMPLEX (HYDROLASE-INHIBITOR), COVALENT COMPLEX, KEYWDS 2 PROTEASE, CATHEPSIN B, HYDROLASE, THIOL PROTEASE, HYDROLASE- KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.D.GREENSPAN,K.L.CLARK,R.A.TOMMASI,S.D.COWEN,L.W.MCQUIRE,D.L.FARLEY, AUTHOR 2 J.H.VAN DUZER,R.L.GOLDBERG,H.ZHOU,Z.DU,J.J.FITT,D.E.COPPA,Z.FANG, AUTHOR 3 W.MACCHIA,L.ZHU,M.P.CAPPARELLI,R.GOLDSTEIN,A.M.WIGG,J.R.DOUGHTY, AUTHOR 4 R.S.BOHACEK,A.K.KNAP REVDAT 3 05-JUL-17 1GMY 1 REMARK REVDAT 2 24-FEB-09 1GMY 1 VERSN REVDAT 1 19-SEP-02 1GMY 0 JRNL AUTH P.D.GREENSPAN,K.L.CLARK,R.A.TOMMASI,S.D.COWEN,L.W.MCQUIRE, JRNL AUTH 2 D.L.FARLEY,J.H.VAN DUZER,R.L.GOLDBERG,H.ZHOU,Z.DU,J.J.FITT, JRNL AUTH 3 D.E.COPPA,Z.FANG,W.MACCHIA,L.ZHU,M.P.CAPPARELLI,R.GOLDSTEIN, JRNL AUTH 4 A.M.WIGG,J.R.DOUGHTY,R.S BOHACEK,A.K.KNAP JRNL TITL IDENTIFICATION OF DIPEPTIDYL NITRILES AS POTENT AND JRNL TITL 2 SELECTIVE INHIBITORS OF CATHEPSIN B THROUGH STRUCTURE-BASED JRNL TITL 3 DRUG DESIGN JRNL REF J.MED.CHEM. V. 44 4524 2001 JRNL REFN ISSN 0022-2623 JRNL PMID 11741472 JRNL DOI 10.1021/JM010206Q REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2000 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 59016 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5971 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8097 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 909 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.007 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5830 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.04 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : BULK SOLVENT MODELING REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.410 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.090 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 50.64 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NII.PARAMETER REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NII.TOPOLOGY REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1290008620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-95 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : YALE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 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) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 83.73333 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 41.86667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 41.86667 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 83.73333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: PQS 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: PQS 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: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C2172 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2203 LIES ON A SPECIAL POSITION. 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 ASP A 254 REMARK 465 GLN A 255 REMARK 465 TYR A 256 REMARK 465 TRP A 257 REMARK 465 GLU A 258 REMARK 465 LYS A 259 REMARK 465 ILE A 260 REMARK 465 THR B 253 REMARK 465 ASP B 254 REMARK 465 GLN B 255 REMARK 465 TYR B 256 REMARK 465 TRP B 257 REMARK 465 GLU B 258 REMARK 465 LYS B 259 REMARK 465 ILE B 260 REMARK 465 THR C 253 REMARK 465 ASP C 254 REMARK 465 GLN C 255 REMARK 465 TYR C 256 REMARK 465 TRP C 257 REMARK 465 GLU C 258 REMARK 465 LYS C 259 REMARK 465 ILE C 260 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 0 CG CD CE NZ REMARK 470 LYS B 0 CG CD CE NZ REMARK 470 LYS C 0 CG CD CE NZ 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 OE2 GLU A 19 O HOH A 2025 2.07 REMARK 500 OE2 GLU C 53 O HOH C 2059 2.13 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 GLU A 122 119.25 -35.27 REMARK 500 PRO A 138 -161.62 -79.84 REMARK 500 ASN A 222 174.91 69.93 REMARK 500 CYS A 240 18.73 58.53 REMARK 500 HIS B 49 47.95 31.30 REMARK 500 THR B 120 -162.13 -107.46 REMARK 500 LYS B 130 53.57 -94.97 REMARK 500 PRO B 138 -162.09 -78.76 REMARK 500 ASN B 222 176.26 67.44 REMARK 500 ALA B 248 -163.25 -160.87 REMARK 500 GLU C 122 113.51 -25.25 REMARK 500 PRO C 138 -155.44 -80.39 REMARK 500 ASN C 222 176.68 68.55 REMARK 500 CYS C 240 16.36 58.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DFA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AEM B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DFA B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AEM C 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APD C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AEM A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DFA C 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CSB RELATED DB: PDB REMARK 900 CATHEPSIN B REMARK 900 RELATED ID: 1HUC RELATED DB: PDB REMARK 900 CATHEPSIN B REMARK 900 RELATED ID: 1PBH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RECOMBINANT PROCATHEPSIN B AT 3.2 REMARK 900 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 2PBH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 3PBH RELATED DB: PDB REMARK 900 REFINED CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 2.5 ANGSTROM REMARK 900 RESOLUTION DBREF 1GMY A 0 260 UNP P07858 CATB_HUMAN 79 339 DBREF 1GMY B 0 260 UNP P07858 CATB_HUMAN 79 339 DBREF 1GMY C 0 260 UNP P07858 CATB_HUMAN 79 339 SEQRES 1 A 261 LYS LEU PRO ALA SER PHE ASP ALA ARG GLU GLN TRP PRO SEQRES 2 A 261 GLN CYS PRO THR ILE LYS GLU ILE ARG ASP GLN GLY SER SEQRES 3 A 261 CYS GLY SER CYS TRP ALA PHE GLY ALA VAL GLU ALA ILE SEQRES 4 A 261 SER ASP ARG ILE CYS ILE HIS THR ASN ALA HIS VAL SER SEQRES 5 A 261 VAL GLU VAL SER ALA GLU ASP LEU LEU THR CYS CYS GLY SEQRES 6 A 261 SER MET CYS GLY ASP GLY CYS ASN GLY GLY TYR PRO ALA SEQRES 7 A 261 GLU ALA TRP ASN PHE TRP THR ARG LYS GLY LEU VAL SER SEQRES 8 A 261 GLY GLY LEU TYR GLU SER HIS VAL GLY CYS ARG PRO TYR SEQRES 9 A 261 SER ILE PRO PRO CYS GLU HIS HIS VAL ASN GLY SER ARG SEQRES 10 A 261 PRO PRO CYS THR GLY GLU GLY ASP THR PRO LYS CYS SER SEQRES 11 A 261 LYS ILE CYS GLU PRO GLY TYR SER PRO THR TYR LYS GLN SEQRES 12 A 261 ASP LYS HIS TYR GLY TYR ASN SER TYR SER VAL SER ASN SEQRES 13 A 261 SER GLU LYS ASP ILE MET ALA GLU ILE TYR LYS ASN GLY SEQRES 14 A 261 PRO VAL GLU GLY ALA PHE SER VAL TYR SER ASP PHE LEU SEQRES 15 A 261 LEU TYR LYS SER GLY VAL TYR GLN HIS VAL THR GLY GLU SEQRES 16 A 261 MET MET GLY GLY HIS ALA ILE ARG ILE LEU GLY TRP GLY SEQRES 17 A 261 VAL GLU ASN GLY THR PRO TYR TRP LEU VAL ALA ASN SER SEQRES 18 A 261 TRP ASN THR ASP TRP GLY ASP ASN GLY PHE PHE LYS ILE SEQRES 19 A 261 LEU ARG GLY GLN ASP HIS CYS GLY ILE GLU SER GLU VAL SEQRES 20 A 261 VAL ALA GLY ILE PRO ARG THR ASP GLN TYR TRP GLU LYS SEQRES 21 A 261 ILE SEQRES 1 B 261 LYS LEU PRO ALA SER PHE ASP ALA ARG GLU GLN TRP PRO SEQRES 2 B 261 GLN CYS PRO THR ILE LYS GLU ILE ARG ASP GLN GLY SER SEQRES 3 B 261 CYS GLY SER CYS TRP ALA PHE GLY ALA VAL GLU ALA ILE SEQRES 4 B 261 SER ASP ARG ILE CYS ILE HIS THR ASN ALA HIS VAL SER SEQRES 5 B 261 VAL GLU VAL SER ALA GLU ASP LEU LEU THR CYS CYS GLY SEQRES 6 B 261 SER MET CYS GLY ASP GLY CYS ASN GLY GLY TYR PRO ALA SEQRES 7 B 261 GLU ALA TRP ASN PHE TRP THR ARG LYS GLY LEU VAL SER SEQRES 8 B 261 GLY GLY LEU TYR GLU SER HIS VAL GLY CYS ARG PRO TYR SEQRES 9 B 261 SER ILE PRO PRO CYS GLU HIS HIS VAL ASN GLY SER ARG SEQRES 10 B 261 PRO PRO CYS THR GLY GLU GLY ASP THR PRO LYS CYS SER SEQRES 11 B 261 LYS ILE CYS GLU PRO GLY TYR SER PRO THR TYR LYS GLN SEQRES 12 B 261 ASP LYS HIS TYR GLY TYR ASN SER TYR SER VAL SER ASN SEQRES 13 B 261 SER GLU LYS ASP ILE MET ALA GLU ILE TYR LYS ASN GLY SEQRES 14 B 261 PRO VAL GLU GLY ALA PHE SER VAL TYR SER ASP PHE LEU SEQRES 15 B 261 LEU TYR LYS SER GLY VAL TYR GLN HIS VAL THR GLY GLU SEQRES 16 B 261 MET MET GLY GLY HIS ALA ILE ARG ILE LEU GLY TRP GLY SEQRES 17 B 261 VAL GLU ASN GLY THR PRO TYR TRP LEU VAL ALA ASN SER SEQRES 18 B 261 TRP ASN THR ASP TRP GLY ASP ASN GLY PHE PHE LYS ILE SEQRES 19 B 261 LEU ARG GLY GLN ASP HIS CYS GLY ILE GLU SER GLU VAL SEQRES 20 B 261 VAL ALA GLY ILE PRO ARG THR ASP GLN TYR TRP GLU LYS SEQRES 21 B 261 ILE SEQRES 1 C 261 LYS LEU PRO ALA SER PHE ASP ALA ARG GLU GLN TRP PRO SEQRES 2 C 261 GLN CYS PRO THR ILE LYS GLU ILE ARG ASP GLN GLY SER SEQRES 3 C 261 CYS GLY SER CYS TRP ALA PHE GLY ALA VAL GLU ALA ILE SEQRES 4 C 261 SER ASP ARG ILE CYS ILE HIS THR ASN ALA HIS VAL SER SEQRES 5 C 261 VAL GLU VAL SER ALA GLU ASP LEU LEU THR CYS CYS GLY SEQRES 6 C 261 SER MET CYS GLY ASP GLY CYS ASN GLY GLY TYR PRO ALA SEQRES 7 C 261 GLU ALA TRP ASN PHE TRP THR ARG LYS GLY LEU VAL SER SEQRES 8 C 261 GLY GLY LEU TYR GLU SER HIS VAL GLY CYS ARG PRO TYR SEQRES 9 C 261 SER ILE PRO PRO CYS GLU HIS HIS VAL ASN GLY SER ARG SEQRES 10 C 261 PRO PRO CYS THR GLY GLU GLY ASP THR PRO LYS CYS SER SEQRES 11 C 261 LYS ILE CYS GLU PRO GLY TYR SER PRO THR TYR LYS GLN SEQRES 12 C 261 ASP LYS HIS TYR GLY TYR ASN SER TYR SER VAL SER ASN SEQRES 13 C 261 SER GLU LYS ASP ILE MET ALA GLU ILE TYR LYS ASN GLY SEQRES 14 C 261 PRO VAL GLU GLY ALA PHE SER VAL TYR SER ASP PHE LEU SEQRES 15 C 261 LEU TYR LYS SER GLY VAL TYR GLN HIS VAL THR GLY GLU SEQRES 16 C 261 MET MET GLY GLY HIS ALA ILE ARG ILE LEU GLY TRP GLY SEQRES 17 C 261 VAL GLU ASN GLY THR PRO TYR TRP LEU VAL ALA ASN SER SEQRES 18 C 261 TRP ASN THR ASP TRP GLY ASP ASN GLY PHE PHE LYS ILE SEQRES 19 C 261 LEU ARG GLY GLN ASP HIS CYS GLY ILE GLU SER GLU VAL SEQRES 20 C 261 VAL ALA GLY ILE PRO ARG THR ASP GLN TYR TRP GLU LYS SEQRES 21 C 261 ILE HET AEM A 500 4 HET APD A 501 12 HET DFA A 502 15 HET AEM B 500 4 HET APD B 501 12 HET DFA B 502 15 HET AEM C 500 4 HET APD C 501 12 HET DFA C 502 15 HETNAM AEM 2-AMINOETHANIMIDIC ACID HETNAM APD 3-METHYLPHENYLALANINE HETNAM DFA DIPHENYLACETIC ACID FORMUL 4 AEM 3(C2 H6 N2) FORMUL 5 APD 3(C10 H13 N O2) FORMUL 6 DFA 3(C14 H12 O2) FORMUL 13 HOH *630(H2 O) HELIX 1 1 ALA A 7 TRP A 11 1 5 HELIX 2 2 CYS A 14 GLU A 19 5 6 HELIX 3 3 SER A 28 THR A 46 1 19 HELIX 4 4 SER A 55 CYS A 63 1 9 HELIX 5 5 GLY A 64 CYS A 67 5 4 HELIX 6 6 ASP A 69 GLY A 73 5 5 HELIX 7 7 TYR A 75 LYS A 86 1 12 HELIX 8 8 THR A 139 LYS A 144 1 6 HELIX 9 9 SER A 156 GLY A 168 1 13 HELIX 10 10 ASP A 179 LEU A 181 5 3 HELIX 11 11 ASP A 238 ILE A 242 5 5 HELIX 12 12 ALA B 7 TRP B 11 1 5 HELIX 13 13 CYS B 14 GLU B 19 5 6 HELIX 14 14 SER B 28 THR B 46 1 19 HELIX 15 15 SER B 55 CYS B 63 1 9 HELIX 16 16 GLY B 64 CYS B 67 5 4 HELIX 17 17 ASP B 69 GLY B 73 5 5 HELIX 18 18 TYR B 75 LYS B 86 1 12 HELIX 19 19 TYR B 140 LYS B 144 5 5 HELIX 20 20 SER B 156 GLY B 168 1 13 HELIX 21 21 ASP B 179 LEU B 181 5 3 HELIX 22 22 ASP B 238 ILE B 242 5 5 HELIX 23 23 ALA C 7 TRP C 11 1 5 HELIX 24 24 CYS C 14 GLU C 19 5 6 HELIX 25 25 SER C 28 THR C 46 1 19 HELIX 26 26 SER C 55 CYS C 63 1 9 HELIX 27 27 GLY C 64 CYS C 67 5 4 HELIX 28 28 ASP C 69 GLY C 73 5 5 HELIX 29 29 TYR C 75 LYS C 86 1 12 HELIX 30 30 THR C 139 LYS C 144 1 6 HELIX 31 31 SER C 156 GLY C 168 1 13 HELIX 32 32 ASP C 179 LEU C 181 5 3 HELIX 33 33 ASP C 238 ILE C 242 5 5 SHEET 1 AA 3 PHE A 5 ASP A 6 0 SHEET 2 AA 3 MET A 195 GLU A 209 -1 O TRP A 206 N PHE A 5 SHEET 3 AA 3 VAL A 170 TYR A 177 -1 O VAL A 170 N ILE A 203 SHEET 1 AB 5 PHE A 5 ASP A 6 0 SHEET 2 AB 5 MET A 195 GLU A 209 -1 O TRP A 206 N PHE A 5 SHEET 3 AB 5 THR A 212 ALA A 218 -1 O THR A 212 N GLU A 209 SHEET 4 AB 5 PHE A 230 LEU A 234 -1 O PHE A 231 N VAL A 217 SHEET 5 AB 5 VAL A 187 TYR A 188 1 O TYR A 188 N LEU A 234 SHEET 1 AC 2 TYR A 151 SER A 152 0 SHEET 2 AC 2 VAL A 247 ALA A 248 -1 O ALA A 248 N TYR A 151 SHEET 1 BA 3 PHE B 5 ASP B 6 0 SHEET 2 BA 3 MET B 195 GLU B 209 -1 O TRP B 206 N PHE B 5 SHEET 3 BA 3 VAL B 170 TYR B 177 -1 O VAL B 170 N ILE B 203 SHEET 1 BB 5 PHE B 5 ASP B 6 0 SHEET 2 BB 5 MET B 195 GLU B 209 -1 O TRP B 206 N PHE B 5 SHEET 3 BB 5 THR B 212 ALA B 218 -1 O THR B 212 N GLU B 209 SHEET 4 BB 5 PHE B 230 LEU B 234 -1 O PHE B 231 N VAL B 217 SHEET 5 BB 5 VAL B 187 TYR B 188 1 O TYR B 188 N LEU B 234 SHEET 1 BC 2 GLY B 147 SER B 152 0 SHEET 2 BC 2 VAL B 247 PRO B 251 -1 O ALA B 248 N TYR B 151 SHEET 1 CA 3 PHE C 5 ASP C 6 0 SHEET 2 CA 3 MET C 195 GLU C 209 -1 O TRP C 206 N PHE C 5 SHEET 3 CA 3 VAL C 170 TYR C 177 -1 O VAL C 170 N ILE C 203 SHEET 1 CB 5 PHE C 5 ASP C 6 0 SHEET 2 CB 5 MET C 195 GLU C 209 -1 O TRP C 206 N PHE C 5 SHEET 3 CB 5 THR C 212 ALA C 218 -1 O THR C 212 N GLU C 209 SHEET 4 CB 5 PHE C 230 LEU C 234 -1 O PHE C 231 N VAL C 217 SHEET 5 CB 5 VAL C 187 TYR C 188 1 O TYR C 188 N LEU C 234 SHEET 1 CC 2 TYR C 151 SER C 152 0 SHEET 2 CC 2 VAL C 247 ALA C 248 -1 O ALA C 248 N TYR C 151 SSBOND 1 CYS A 14 CYS A 43 1555 1555 2.02 SSBOND 2 CYS A 26 CYS A 71 1555 1555 2.03 SSBOND 3 CYS A 62 CYS A 128 1555 1555 2.05 SSBOND 4 CYS A 63 CYS A 67 1555 1555 2.02 SSBOND 5 CYS A 100 CYS A 132 1555 1555 2.04 SSBOND 6 CYS A 108 CYS A 119 1555 1555 2.03 SSBOND 7 CYS B 14 CYS B 43 1555 1555 2.03 SSBOND 8 CYS B 26 CYS B 71 1555 1555 2.04 SSBOND 9 CYS B 62 CYS B 128 1555 1555 2.04 SSBOND 10 CYS B 63 CYS B 67 1555 1555 2.03 SSBOND 11 CYS B 100 CYS B 132 1555 1555 2.03 SSBOND 12 CYS B 108 CYS B 119 1555 1555 2.03 SSBOND 13 CYS C 14 CYS C 43 1555 1555 2.05 SSBOND 14 CYS C 26 CYS C 71 1555 1555 2.03 SSBOND 15 CYS C 62 CYS C 128 1555 1555 2.05 SSBOND 16 CYS C 63 CYS C 67 1555 1555 2.02 SSBOND 17 CYS C 100 CYS C 132 1555 1555 2.03 SSBOND 18 CYS C 108 CYS C 119 1555 1555 2.03 LINK SG CYS A 29 C1 AEM A 500 1555 1555 1.82 LINK N2 AEM A 500 C APD A 501 1555 1555 1.33 LINK N APD A 501 C8 DFA A 502 1555 1555 1.32 LINK SG CYS B 29 C1 AEM B 500 1555 1555 1.79 LINK N2 AEM B 500 C APD B 501 1555 1555 1.33 LINK N APD B 501 C8 DFA B 502 1555 1555 1.33 LINK SG CYS C 29 C1 AEM C 500 1555 1555 1.79 LINK N2 AEM C 500 C APD C 501 1555 1555 1.34 LINK N APD C 501 C8 DFA C 502 1555 1555 1.33 CISPEP 1 SER A 137 PRO A 138 0 0.52 CISPEP 2 SER B 137 PRO B 138 0 0.35 CISPEP 3 SER C 137 PRO C 138 0 0.47 SITE 1 AC1 13 CYS A 29 TRP A 30 GLY A 73 GLY A 74 SITE 2 AC1 13 PRO A 76 ALA A 173 GLY A 198 HIS A 199 SITE 3 AC1 13 GLU A 245 AEM A 500 DFA A 502 GLU B 245 SITE 4 AC1 13 DFA B 502 SITE 1 AC2 11 ASP A 69 ASN A 72 GLY A 73 GLY A 74 SITE 2 AC2 11 TYR A 75 APD A 501 HOH A2181 MET B 195 SITE 3 AC2 11 GLY B 198 APD B 501 DFA B 502 SITE 1 AC3 6 GLN B 23 GLY B 27 CYS B 29 GLY B 198 SITE 2 AC3 6 APD B 501 HOH B2106 SITE 1 AC4 11 SER A 175 GLY A 198 APD A 501 DFA A 502 SITE 2 AC4 11 ASP B 69 ASN B 72 GLY B 73 GLY B 74 SITE 3 AC4 11 TYR B 75 APD B 501 HOH B2170 SITE 1 AC5 7 GLN C 23 GLY C 27 SER C 28 CYS C 29 SITE 2 AC5 7 GLY C 198 APD C 501 HOH C2213 SITE 1 AC6 12 CYS C 29 TRP C 30 GLY C 73 GLY C 74 SITE 2 AC6 12 PRO C 76 ALA C 173 GLY C 198 HIS C 199 SITE 3 AC6 12 AEM C 500 DFA C 502 HOH C2148 HOH C2150 SITE 1 AC7 6 GLN A 23 GLY A 27 CYS A 29 GLY A 198 SITE 2 AC7 6 APD A 501 HOH A2212 SITE 1 AC8 12 GLU A 245 DFA A 502 CYS B 29 TRP B 30 SITE 2 AC8 12 GLY B 73 GLY B 74 PRO B 76 ALA B 173 SITE 3 AC8 12 GLY B 198 HIS B 199 AEM B 500 DFA B 502 SITE 1 AC9 5 ASN C 72 GLY C 73 GLY C 74 TYR C 75 SITE 2 AC9 5 APD C 501 CRYST1 103.900 103.900 125.600 90.00 90.00 120.00 P 32 2 1 18 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 0.009625 0.005557 0.000000 0.00000 SCALE2 0.000000 0.011113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007962 0.00000