PDB Short entry for 4CIA HEADER HYDROLASE 06-DEC-13 4CIA TITLE CRYSTAL STRUCTURE OF CATHEPSIN A, COMPLEXED WITH COMPOUND 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOSOMAL PROTECTIVE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBOXYPEPTIDASE C, CARBOXYPEPTIDASE L, CATHEPSIN A, COMPND 5 PROTECTIVE PROTEIN CATHEPSIN A, PPCA, PROTECTIVE PROTEIN FOR BETA- COMPND 6 GALACTOSIDASE; COMPND 7 EC: 3.4.16.5; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: ACTIVATED WITH TRYPSIN-SEPHAROSE 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; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS PVL1393 KEYWDS HYDROLASE, SERINE CARBOXYPEPTIDASE, CARDIOVASCULAR DRUG, HEART KEYWDS 2 FAILURE, ENDOTHELIN, TETRAHEDRAL INTERMEDIATE, COVALENT INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR H.A.SCHREUDER,A.LIESUM,K.KROLL,B.BOEHNISCH,C.BUNING,S.RUF,C.BUNING, AUTHOR 2 T.SADOWSKI REVDAT 5 20-DEC-23 4CIA 1 HETSYN REVDAT 4 29-JUL-20 4CIA 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-MAR-19 4CIA 1 JRNL REMARK LINK REVDAT 2 02-APR-14 4CIA 1 JRNL REVDAT 1 26-FEB-14 4CIA 0 JRNL AUTH H.A.SCHREUDER,A.LIESUM,K.KROLL,B.BOHNISCH,C.BUNING,S.RUF, JRNL AUTH 2 T.SADOWSKI JRNL TITL CRYSTAL STRUCTURE OF CATHEPSIN A, A NOVEL TARGET FOR THE JRNL TITL 2 TREATMENT OF CARDIOVASCULAR DISEASES. JRNL REF BIOCHEM. BIOPHYS. RES. V. 445 451 2014 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 24530914 JRNL DOI 10.1016/J.BBRC.2014.02.014 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.RUF,C.BUNING,H.SCHREUDER,G.HORSTICK,W.LINZ,T.OLPP, REMARK 1 AUTH 2 J.PERNERSTORFER,K.HISS,K.KROLL,A.KANNT,M.KOHLMANN,D.LINZ, REMARK 1 AUTH 3 T.HUBSCHLE,H.RUTTEN,K.WIRTH,T.SCHMIDT,T.SADOWSKI REMARK 1 TITL NOVEL BETA-AMINO ACID DERIVATIVES AS INHIBITORS OF CATHEPSIN REMARK 1 TITL 2 A. REMARK 1 REF J.MED.CHEM. V. 55 7636 2012 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 22861813 REMARK 1 DOI 10.1021/JM300663N REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 27298 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1437 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1598 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3273 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.150 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3442 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4685 ; 1.706 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 6.621 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;37.292 ;24.819 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 530 ;14.197 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.426 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 491 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2693 ; 0.008 ; 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): NULL ; NULL ; NULL 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4CIA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1290059178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28737 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 66.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4AZ0 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CATHEPSIN A WAS CRYSTALLIZED USING THE REMARK 280 HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ REMARK 280 ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS REMARK 280 MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE REMARK 280 (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE REMARK 280 AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK., PH REMARK 280 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.05300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.64750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.05300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.64750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.7 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 -90.10600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A2009 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2206 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 SER A -1 REMARK 465 SER A 259 REMARK 465 HIS A 260 REMARK 465 PHE A 261 REMARK 465 ARG A 262 REMARK 465 TYR A 263 REMARK 465 GLU A 264 REMARK 465 LYS A 265 REMARK 465 ASP A 266 REMARK 465 THR A 267 REMARK 465 VAL A 268 REMARK 465 VAL A 269 REMARK 465 VAL A 270 REMARK 465 GLN A 271 REMARK 465 ASP A 272 REMARK 465 LEU A 273 REMARK 465 GLY A 274 REMARK 465 ASN A 275 REMARK 465 ILE A 276 REMARK 465 PHE A 277 REMARK 465 THR A 278 REMARK 465 ARG A 279 REMARK 465 LEU A 280 REMARK 465 PRO A 281 REMARK 465 LEU A 282 REMARK 465 LYS A 283 REMARK 465 ARG A 284 REMARK 465 MET A 285 REMARK 465 TRP A 286 REMARK 465 HIS A 287 REMARK 465 GLN A 288 REMARK 465 ALA A 289 REMARK 465 LEU A 290 REMARK 465 LEU A 291 REMARK 465 ARG A 292 REMARK 465 SER A 293 REMARK 465 GLY A 294 REMARK 465 ASP A 295 REMARK 465 LYS A 296 REMARK 465 VAL A 297 REMARK 465 ARG A 298 REMARK 465 ASP A 404 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 ARG A 0 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 ARG A 9 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 ASN A 188 CG REMARK 470 PRO A 258 CA C O CB CG CD 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 LEU A 226 O HOH A 2204 1.47 REMARK 500 O HOH A 2162 O HOH A 2163 1.71 REMARK 500 CB SER A 206 O HOH A 2188 1.82 REMARK 500 CB SER A 386 O HOH A 2166 1.83 REMARK 500 OG1 THR A 230 O HOH A 2205 2.06 REMARK 500 CB ASN A 90 O HOH A 2049 2.06 REMARK 500 CA LEU A 226 O HOH A 2201 2.08 REMARK 500 O HOH A 2119 O HOH A 2121 2.12 REMARK 500 O HOH A 2153 O HOH A 2291 2.13 REMARK 500 O HOH A 2231 O HOH A 2232 2.15 REMARK 500 CZ2 TRP A 205 O HOH A 2178 2.15 REMARK 500 O ALA A 152 O HOH A 2140 2.19 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 A 2128 O HOH A 2128 2556 1.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 110 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 LEU A 174 CA - CB - CG ANGL. DEV. = 22.3 DEGREES REMARK 500 LEU A 174 CB - CG - CD1 ANGL. DEV. = 11.5 DEGREES REMARK 500 LEU A 226 CA - CB - CG ANGL. DEV. = -17.0 DEGREES REMARK 500 ILE A 246 CB - CA - C ANGL. DEV. = -14.6 DEGREES 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 69 -70.62 -113.47 REMARK 500 SER A 150 -125.07 68.11 REMARK 500 ALA A 152 -8.99 -59.62 REMARK 500 GLN A 215 -125.56 33.63 REMARK 500 TYR A 221 -61.34 -102.98 REMARK 500 ASN A 248 93.89 -169.62 REMARK 500 ASP A 300 72.99 -175.86 REMARK 500 MET A 430 77.07 -105.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1461 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 3 OD2 REMARK 620 2 HIS A 211 ND1 101.8 REMARK 620 3 ASP A 225 OD2 107.8 131.1 REMARK 620 4 ASP A 225 OD1 86.1 94.5 50.9 REMARK 620 5 HOH A2002 O 75.6 157.8 69.2 107.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1460 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 179 O REMARK 620 2 HOH A2158 O 129.0 REMARK 620 3 HOH A2169 O 131.7 87.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1456 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 184 OE2 REMARK 620 2 CD A1458 CD 117.7 REMARK 620 3 HOH A2162 O 71.0 128.9 REMARK 620 4 HOH A2163 O 71.2 171.1 50.7 REMARK 620 5 HOH A2255 O 114.4 63.6 163.7 115.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1459 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 186 OD1 REMARK 620 2 ALA A 374 O 76.0 REMARK 620 3 CYS A 375 SG 145.7 81.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1458 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 222 OD2 REMARK 620 2 ASP A 222 OD1 48.5 REMARK 620 3 GLU A 326 OE1 122.5 162.0 REMARK 620 4 GLU A 326 OE2 77.1 117.8 47.1 REMARK 620 5 HOH A2255 O 73.0 104.0 84.7 81.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1457 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 225 OD2 REMARK 620 2 CD A1461 CD 46.3 REMARK 620 3 CD A1461 CD 51.0 73.6 REMARK 620 4 HOH A2352 O 117.0 143.7 124.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1455 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 434 OD2 REMARK 620 2 ASP A 434 OD1 47.7 REMARK 620 3 HOH A2220 O 71.2 115.0 REMARK 620 4 HOH A2224 O 113.5 109.1 114.4 REMARK 620 5 HOH A2351 O 145.1 111.6 106.2 99.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CI9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATHEPSIN A, APO-STRUCTURE REMARK 900 RELATED ID: 4CIB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATHEPSIN A, COMPLEXED WITH COMPOUND 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AT THE N-TERMINUS, 2 RESIDUES FROM PREPROMELLITIN SIGNAL REMARK 999 SEQUENCE ARE PRESENT, AT THE C-TERMINUS, 1 RESIDUE LEFT REMARK 999 OVER FROM THE MYC-TAG IS PRESENT. DBREF 4CIA A 1 452 UNP P10619 PPGB_HUMAN 29 480 SEQADV 4CIA SER A -1 UNP P10619 EXPRESSION TAG SEQADV 4CIA ARG A 0 UNP P10619 EXPRESSION TAG SEQADV 4CIA GLU A 453 UNP P10619 EXPRESSION TAG SEQRES 1 A 455 SER ARG ALA PRO ASP GLN ASP GLU ILE GLN ARG LEU PRO SEQRES 2 A 455 GLY LEU ALA LYS GLN PRO SER PHE ARG GLN TYR SER GLY SEQRES 3 A 455 TYR LEU LYS GLY SER GLY SER LYS HIS LEU HIS TYR TRP SEQRES 4 A 455 PHE VAL GLU SER GLN LYS ASP PRO GLU ASN SER PRO VAL SEQRES 5 A 455 VAL LEU TRP LEU ASN GLY GLY PRO GLY CYS SER SER LEU SEQRES 6 A 455 ASP GLY LEU LEU THR GLU HIS GLY PRO PHE LEU VAL GLN SEQRES 7 A 455 PRO ASP GLY VAL THR LEU GLU TYR ASN PRO TYR SER TRP SEQRES 8 A 455 ASN LEU ILE ALA ASN VAL LEU TYR LEU GLU SER PRO ALA SEQRES 9 A 455 GLY VAL GLY PHE SER TYR SER ASP ASP LYS PHE TYR ALA SEQRES 10 A 455 THR ASN ASP THR GLU VAL ALA GLN SER ASN PHE GLU ALA SEQRES 11 A 455 LEU GLN ASP PHE PHE ARG LEU PHE PRO GLU TYR LYS ASN SEQRES 12 A 455 ASN LYS LEU PHE LEU THR GLY GLU SER TYR ALA GLY ILE SEQRES 13 A 455 TYR ILE PRO THR LEU ALA VAL LEU VAL MET GLN ASP PRO SEQRES 14 A 455 SER MET ASN LEU GLN GLY LEU ALA VAL GLY ASN GLY LEU SEQRES 15 A 455 SER SER TYR GLU GLN ASN ASP ASN SER LEU VAL TYR PHE SEQRES 16 A 455 ALA TYR TYR HIS GLY LEU LEU GLY ASN ARG LEU TRP SER SEQRES 17 A 455 SER LEU GLN THR HIS CYS CYS SER GLN ASN LYS CYS ASN SEQRES 18 A 455 PHE TYR ASP ASN LYS ASP LEU GLU CYS VAL THR ASN LEU SEQRES 19 A 455 GLN GLU VAL ALA ARG ILE VAL GLY ASN SER GLY LEU ASN SEQRES 20 A 455 ILE TYR ASN LEU TYR ALA PRO CYS ALA GLY GLY VAL PRO SEQRES 21 A 455 SER HIS PHE ARG TYR GLU LYS ASP THR VAL VAL VAL GLN SEQRES 22 A 455 ASP LEU GLY ASN ILE PHE THR ARG LEU PRO LEU LYS ARG SEQRES 23 A 455 MET TRP HIS GLN ALA LEU LEU ARG SER GLY ASP LYS VAL SEQRES 24 A 455 ARG MET ASP PRO PRO CYS THR ASN THR THR ALA ALA SER SEQRES 25 A 455 THR TYR LEU ASN ASN PRO TYR VAL ARG LYS ALA LEU ASN SEQRES 26 A 455 ILE PRO GLU GLN LEU PRO GLN TRP ASP MET CYS ASN PHE SEQRES 27 A 455 LEU VAL ASN LEU GLN TYR ARG ARG LEU TYR ARG SER MET SEQRES 28 A 455 ASN SER GLN TYR LEU LYS LEU LEU SER SER GLN LYS TYR SEQRES 29 A 455 GLN ILE LEU LEU TYR ASN GLY ASP VAL ASP MET ALA CYS SEQRES 30 A 455 ASN PHE MET GLY ASP GLU TRP PHE VAL ASP SER LEU ASN SEQRES 31 A 455 GLN LYS MET GLU VAL GLN ARG ARG PRO TRP LEU VAL LYS SEQRES 32 A 455 TYR GLY ASP SER GLY GLU GLN ILE ALA GLY PHE VAL LYS SEQRES 33 A 455 GLU PHE SER HIS ILE ALA PHE LEU THR ILE LYS GLY ALA SEQRES 34 A 455 GLY HIS MET VAL PRO THR ASP LYS PRO LEU ALA ALA PHE SEQRES 35 A 455 THR MET PHE SER ARG PHE LEU ASN LYS GLN PRO TYR GLU MODRES 4CIA ASN A 117 ASN GLYCOSYLATION SITE MODRES 4CIA ASN A 305 ASN GLYCOSYLATION SITE HET 6KZ A1454 33 HET CD A1455 1 HET CD A1456 1 HET CD A1457 1 HET CD A1458 1 HET CD A1459 1 HET CD A1460 1 HET CD A1461 1 HET NAG A3010 14 HET NAG A3020 14 HETNAM 6KZ N-[(2S)-4-METHYL-1-OXIDANYLIDENE-1-[[(1R,2S)-1- HETNAM 2 6KZ OXIDANYL-1-(5-PHENYL-1,2,4-OXADIAZOL-3-YL)BUTAN-2- HETNAM 3 6KZ YL]AMINO]PENTAN-2-YL]MORPHOLINE-4-CARBOXAMIDE HETNAM CD CADMIUM ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 6KZ C23 H33 N5 O5 FORMUL 3 CD 7(CD 2+) FORMUL 10 NAG 2(C8 H15 N O6) FORMUL 12 HOH *358(H2 O) HELIX 1 1 PRO A 2 ASP A 5 5 4 HELIX 2 2 SER A 62 GLU A 69 1 8 HELIX 3 3 SER A 88 ILE A 92 5 5 HELIX 4 4 ASN A 117 PHE A 136 1 20 HELIX 5 5 PRO A 137 LYS A 140 5 4 HELIX 6 6 TYR A 151 MET A 164 1 14 HELIX 7 7 SER A 182 HIS A 197 1 16 HELIX 8 8 GLY A 201 CYS A 212 1 12 HELIX 9 9 ASP A 225 ASN A 241 1 17 HELIX 10 10 THR A 306 ASN A 314 1 9 HELIX 11 11 ASN A 315 LEU A 322 1 8 HELIX 12 12 ASN A 335 TYR A 342 1 8 HELIX 13 13 MET A 349 SER A 359 1 11 HELIX 14 14 ASN A 376 LEU A 387 1 12 HELIX 15 15 MET A 430 LYS A 435 1 6 HELIX 16 16 LYS A 435 ASN A 448 1 14 SHEET 1 AA 2 GLN A 21 LYS A 27 0 SHEET 2 AA 2 LYS A 32 VAL A 39 -1 O LEU A 34 N LEU A 26 SHEET 1 AB 2 TYR A 108 SER A 109 0 SHEET 2 AB 2 LYS A 32 VAL A 39 1 O HIS A 33 N TYR A 108 SHEET 1 AC10 ARG A 396 LYS A 401 0 SHEET 2 AC10 GLU A 407 PHE A 416 -1 O GLN A 408 N VAL A 400 SHEET 3 AC10 ILE A 419 ILE A 424 -1 O ILE A 419 N PHE A 416 SHEET 4 AC10 GLN A 363 GLY A 369 1 O ILE A 364 N ALA A 420 SHEET 5 AC10 LEU A 171 GLY A 177 1 O GLN A 172 N GLN A 363 SHEET 6 AC10 LEU A 144 GLU A 149 1 O LEU A 144 N GLN A 172 SHEET 7 AC10 VAL A 50 LEU A 54 1 O VAL A 50 N PHE A 145 SHEET 8 AC10 ASN A 94 LEU A 98 1 O ASN A 94 N VAL A 51 SHEET 9 AC10 LYS A 32 VAL A 39 -1 O TRP A 37 N TYR A 97 SHEET 10 AC10 TYR A 108 SER A 109 1 O TYR A 108 N HIS A 33 SHEET 1 AD10 ARG A 396 LYS A 401 0 SHEET 2 AD10 GLU A 407 PHE A 416 -1 O GLN A 408 N VAL A 400 SHEET 3 AD10 ILE A 419 ILE A 424 -1 O ILE A 419 N PHE A 416 SHEET 4 AD10 GLN A 363 GLY A 369 1 O ILE A 364 N ALA A 420 SHEET 5 AD10 LEU A 171 GLY A 177 1 O GLN A 172 N GLN A 363 SHEET 6 AD10 LEU A 144 GLU A 149 1 O LEU A 144 N GLN A 172 SHEET 7 AD10 VAL A 50 LEU A 54 1 O VAL A 50 N PHE A 145 SHEET 8 AD10 ASN A 94 LEU A 98 1 O ASN A 94 N VAL A 51 SHEET 9 AD10 LYS A 32 VAL A 39 -1 O TRP A 37 N TYR A 97 SHEET 10 AD10 GLN A 21 LYS A 27 -1 O TYR A 22 N PHE A 38 SHEET 1 AE 2 PHE A 73 VAL A 75 0 SHEET 2 AE 2 LEU A 82 TYR A 84 -1 O GLU A 83 N LEU A 74 SHEET 1 AF 2 CYS A 213 SER A 214 0 SHEET 2 AF 2 LYS A 217 CYS A 218 -1 O LYS A 217 N SER A 214 SSBOND 1 CYS A 60 CYS A 334 1555 1555 2.03 SSBOND 2 CYS A 212 CYS A 228 1555 1555 2.04 SSBOND 3 CYS A 213 CYS A 218 1555 1555 2.06 SSBOND 4 CYS A 253 CYS A 303 1555 1555 2.02 LINK ND2 ASN A 117 C1 NAG A3010 1555 1555 1.45 LINK OG SER A 150 C15 6KZ A1454 1555 1555 1.45 LINK ND2 ASN A 305 C1 NAG A3020 1555 1555 1.44 LINK OD2 ASP A 3 CD CD A1461 1555 1555 2.21 LINK O GLY A 179 CD CD A1460 1555 1555 2.57 LINK OE2 GLU A 184 CD CD A1456 1555 1555 2.60 LINK OD1 ASN A 186 CD CD A1459 1555 1555 2.98 LINK ND1 HIS A 211 CD CD A1461 3545 1555 2.53 LINK OD2 ASP A 222 CD CD A1458 1555 1555 2.81 LINK OD1 ASP A 222 CD CD A1458 1555 1555 2.45 LINK OD2 ASP A 225 CD CD A1457 1555 1555 3.13 LINK OD2 ASP A 225 CD CD A1461 3545 1555 2.26 LINK OD1 ASP A 225 CD CD A1461 3545 1555 2.73 LINK OE1 GLU A 326 CD CD A1458 4456 1555 2.88 LINK OE2 GLU A 326 CD CD A1458 4456 1555 2.61 LINK O ALA A 374 CD CD A1459 1555 1555 2.74 LINK SG CYS A 375 CD CD A1459 1555 1555 2.51 LINK OD2 ASP A 434 CD CD A1455 1555 1555 2.88 LINK OD1 ASP A 434 CD CD A1455 1555 1555 2.42 LINK CD CD A1455 O HOH A2220 1555 1555 2.47 LINK CD CD A1455 O HOH A2224 1555 1555 2.42 LINK CD CD A1455 O HOH A2351 1555 1555 3.19 LINK CD CD A1456 CD CD A1458 1555 1555 2.50 LINK CD CD A1456 O HOH A2162 1555 1555 1.81 LINK CD CD A1456 O HOH A2163 1555 1555 2.13 LINK CD CD A1456 O HOH A2255 1555 4456 1.83 LINK CD CD A1457 CD CD A1461 1555 3455 2.05 LINK CD CD A1457 CD CD A1461 3545 1555 2.05 LINK CD CD A1457 O HOH A2352 1555 1555 2.26 LINK CD CD A1458 O HOH A2255 1555 4456 2.35 LINK CD CD A1460 O HOH A2158 1555 1555 2.80 LINK CD CD A1460 O HOH A2169 1555 1555 2.65 LINK CD CD A1461 O HOH A2002 1555 1555 2.88 CISPEP 1 GLY A 57 PRO A 58 0 -2.77 CISPEP 2 SER A 100 PRO A 101 0 2.71 CRYST1 90.106 101.295 48.077 90.00 101.91 90.00 C 1 2 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 0.011098 0.000000 0.002341 0.00000 SCALE2 0.000000 0.009872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021258 0.00000