PDB Short entry for 4AZ3 HEADER HYDROLASE 22-JUN-12 4AZ3 TITLE CRYSTAL STRUCTURE OF CATHEPSIN A, COMPLEXED WITH 15A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACTIVATED PROTEASE RESIDUES 29-326; COMPND 5 SYNONYM: LYSOSOMAL PROTECTIVE PROTEIN CARBOXYPEPTIDASE C, COMPND 6 CARBOXYPEPTIDASE L, CATHEPSIN A, PROTECTIVE PROTEIN CATHEPSIN A, COMPND 7 PPCA, PROTECTIVE PROTEIN FOR BETA-GALACTOSIDASE; COMPND 8 EC: 3.4.16.5; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: ACTIVATED WITH TRYPSIN-SEPHAROSE; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAIN; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: ACTIVATED PROTEASE, RESIDUES 327-480; COMPND 15 SYNONYM: LYSOSOMAL PROTECTIVE PROTEIN CARBOXYPEPTIDASE C, COMPND 16 CARBOXYPEPTIDASE L, CATHEPSIN A, PROTECTIVE PROTEIN CATHEPSIN A, COMPND 17 PPCA, PROTECTIVE PROTEIN FOR BETA-GALACTOSIDASE; COMPND 18 EC: 3.4.16.5; COMPND 19 ENGINEERED: YES; COMPND 20 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: PVL1393; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 16 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PVL1393 KEYWDS HYDROLASE, DRUG DISCOVERY, CARBOXYPEPTIDASE, CARDIOVASCULAR EXPDTA X-RAY DIFFRACTION AUTHOR S.RUF,C.BUNING,H.SCHREUDER,G.HORSTICK,W.LINZ,T.OLPP,J.PERNERSTORFER, AUTHOR 2 K.HISS,K.KROLL,A.KANNT,M.KOHLMANN,D.LINZ,T.HUEBSCHLE,H.RUETTEN, AUTHOR 3 K.WIRTH,T.SCHMIDT,T.SADOWSKI REVDAT 5 20-DEC-23 4AZ3 1 HETSYN REVDAT 4 29-JUL-20 4AZ3 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 08-MAY-19 4AZ3 1 REMARK REVDAT 2 03-APR-19 4AZ3 1 REMARK LINK REVDAT 1 26-SEP-12 4AZ3 0 JRNL AUTH S.RUF,C.BUNING,H.SCHREUDER,G.HORSTICK,W.LINZ,T.OLPP, JRNL AUTH 2 J.PERNERSTORFER,K.HISS,K.KROLL,A.KANNT,M.KOHLMANN,D.LINZ, JRNL AUTH 3 T.HUBSCHLE,H.RUTTEN,K.WIRTH,T.SCHMIDT,T.SADOWSKI JRNL TITL NOVEL BETA-AMINO ACID DERIVATIVES AS INHIBITORS OF CATHEPSIN JRNL TITL 2 A. JRNL REF J.MED.CHEM. V. 55 7636 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22861813 JRNL DOI 10.1021/JM300663N REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 27378 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1344 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 14 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.05 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2892 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2409 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2762 REMARK 3 BIN R VALUE (WORKING SET) : 0.2405 REMARK 3 BIN FREE R VALUE : 0.2506 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 130 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3288 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 95 REMARK 3 SOLVENT ATOMS : 422 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50780 REMARK 3 B22 (A**2) : -0.59040 REMARK 3 B33 (A**2) : 1.09810 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.10750 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.244 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.234 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.167 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.218 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.164 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3533 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4823 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1183 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 95 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 507 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3533 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 436 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 3 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4443 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.38 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.46 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP. REMARK 3 RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD. NUMBER OF REMARK 3 ATOMS WITH PROPER CCP4 ATOM TYPE=3850. NUMBER WITH APPROX REMARK 3 DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED REMARK 3 CONTACTS=4. REMARK 4 REMARK 4 4AZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290053025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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) : 0.9395 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27381 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 67.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: MODEL DERIVED FROM PDB ENTRY 1IVY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CATA 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 4 DEG. 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 45.29500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.29500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.40000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 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 A2207 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 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 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 -76.70 -106.95 REMARK 500 PRO A 101 -168.47 -75.57 REMARK 500 SER A 150 -111.10 56.24 REMARK 500 GLN A 215 -86.25 57.64 REMARK 500 TYR A 221 -61.45 -98.51 REMARK 500 ASN A 248 102.19 -162.04 REMARK 500 MET B 430 76.63 -110.70 REMARK 500 MET B 430 78.08 -109.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2016 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B2151 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH B2152 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH B2153 DISTANCE = 6.66 ANGSTROMS 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 A1261 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 3 OD2 REMARK 620 2 ASP A 3 OD1 56.0 REMARK 620 3 HIS A 211 ND1 112.5 86.9 REMARK 620 4 ASP A 225 OD1 72.5 124.6 95.9 REMARK 620 5 ASP A 225 OD2 87.7 134.6 135.7 51.5 REMARK 620 6 HOH A2220 O 137.3 97.8 97.1 136.1 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1260 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 184 OE2 REMARK 620 2 GLU A 184 OE1 44.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1262 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 222 OD2 REMARK 620 2 ASP A 222 OD1 49.9 REMARK 620 3 GLU B 326 OE2 90.0 120.3 REMARK 620 4 GLU B 326 OE1 122.2 166.0 45.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B1454 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 374 O REMARK 620 2 CYS B 375 SG 92.5 REMARK 620 3 HOH B2091 O 79.0 139.0 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IVY RELATED DB: PDB REMARK 900 PHYSIOLOGICAL DIMER HPP PRECURSOR REMARK 900 RELATED ID: 4AZ0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATHEPSIN A, COMPLEXED WITH 8A. REMARK 999 REMARK 999 SEQUENCE REMARK 999 EXTRA C-TERMINAL GLU AS LEFTOVER FROM MYC-TAG DBREF 4AZ3 A 1 298 UNP P10619 PPGB_HUMAN 29 326 DBREF 4AZ3 B 299 452 UNP P10619 PPGB_HUMAN 327 480 SEQADV 4AZ3 SER A -1 UNP P10619 EXPRESSION TAG SEQADV 4AZ3 ARG A 0 UNP P10619 EXPRESSION TAG SEQADV 4AZ3 GLU B 453 UNP P10619 EXPRESSION TAG SEQRES 1 A 300 SER ARG ALA PRO ASP GLN ASP GLU ILE GLN ARG LEU PRO SEQRES 2 A 300 GLY LEU ALA LYS GLN PRO SER PHE ARG GLN TYR SER GLY SEQRES 3 A 300 TYR LEU LYS GLY SER GLY SER LYS HIS LEU HIS TYR TRP SEQRES 4 A 300 PHE VAL GLU SER GLN LYS ASP PRO GLU ASN SER PRO VAL SEQRES 5 A 300 VAL LEU TRP LEU ASN GLY GLY PRO GLY CYS SER SER LEU SEQRES 6 A 300 ASP GLY LEU LEU THR GLU HIS GLY PRO PHE LEU VAL GLN SEQRES 7 A 300 PRO ASP GLY VAL THR LEU GLU TYR ASN PRO TYR SER TRP SEQRES 8 A 300 ASN LEU ILE ALA ASN VAL LEU TYR LEU GLU SER PRO ALA SEQRES 9 A 300 GLY VAL GLY PHE SER TYR SER ASP ASP LYS PHE TYR ALA SEQRES 10 A 300 THR ASN ASP THR GLU VAL ALA GLN SER ASN PHE GLU ALA SEQRES 11 A 300 LEU GLN ASP PHE PHE ARG LEU PHE PRO GLU TYR LYS ASN SEQRES 12 A 300 ASN LYS LEU PHE LEU THR GLY GLU SER TYR ALA GLY ILE SEQRES 13 A 300 TYR ILE PRO THR LEU ALA VAL LEU VAL MET GLN ASP PRO SEQRES 14 A 300 SER MET ASN LEU GLN GLY LEU ALA VAL GLY ASN GLY LEU SEQRES 15 A 300 SER SER TYR GLU GLN ASN ASP ASN SER LEU VAL TYR PHE SEQRES 16 A 300 ALA TYR TYR HIS GLY LEU LEU GLY ASN ARG LEU TRP SER SEQRES 17 A 300 SER LEU GLN THR HIS CYS CYS SER GLN ASN LYS CYS ASN SEQRES 18 A 300 PHE TYR ASP ASN LYS ASP LEU GLU CYS VAL THR ASN LEU SEQRES 19 A 300 GLN GLU VAL ALA ARG ILE VAL GLY ASN SER GLY LEU ASN SEQRES 20 A 300 ILE TYR ASN LEU TYR ALA PRO CYS ALA GLY GLY VAL PRO SEQRES 21 A 300 SER HIS PHE ARG TYR GLU LYS ASP THR VAL VAL VAL GLN SEQRES 22 A 300 ASP LEU GLY ASN ILE PHE THR ARG LEU PRO LEU LYS ARG SEQRES 23 A 300 MET TRP HIS GLN ALA LEU LEU ARG SER GLY ASP LYS VAL SEQRES 24 A 300 ARG SEQRES 1 B 155 MET ASP PRO PRO CYS THR ASN THR THR ALA ALA SER THR SEQRES 2 B 155 TYR LEU ASN ASN PRO TYR VAL ARG LYS ALA LEU ASN ILE SEQRES 3 B 155 PRO GLU GLN LEU PRO GLN TRP ASP MET CYS ASN PHE LEU SEQRES 4 B 155 VAL ASN LEU GLN TYR ARG ARG LEU TYR ARG SER MET ASN SEQRES 5 B 155 SER GLN TYR LEU LYS LEU LEU SER SER GLN LYS TYR GLN SEQRES 6 B 155 ILE LEU LEU TYR ASN GLY ASP VAL ASP MET ALA CYS ASN SEQRES 7 B 155 PHE MET GLY ASP GLU TRP PHE VAL ASP SER LEU ASN GLN SEQRES 8 B 155 LYS MET GLU VAL GLN ARG ARG PRO TRP LEU VAL LYS TYR SEQRES 9 B 155 GLY ASP SER GLY GLU GLN ILE ALA GLY PHE VAL LYS GLU SEQRES 10 B 155 PHE SER HIS ILE ALA PHE LEU THR ILE LYS GLY ALA GLY SEQRES 11 B 155 HIS MET VAL PRO THR ASP LYS PRO LEU ALA ALA PHE THR SEQRES 12 B 155 MET PHE SER ARG PHE LEU ASN LYS GLN PRO TYR GLU MODRES 4AZ3 ASN A 117 ASN GLYCOSYLATION SITE MODRES 4AZ3 ASN B 305 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET S35 A1259 70 HET CD A1260 1 HET CD A1261 1 HET CD A1262 1 HET CD B1454 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM S35 (3S)-3-({[1-(2-FLUOROPHENYL)-5-{[(2R)-2-HYDROXY-3,3- HETNAM 2 S35 DIMETHYLBUTYL]OXY}-1H-PYRAZOL-3-YL]CARBONYL}AMINO)-3- HETNAM 3 S35 (2-METHYLPHENYL)PROPANOIC ACID HETNAM CD CADMIUM ION 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 3 NAG 4(C8 H15 N O6) FORMUL 5 S35 C26 H30 F N3 O5 FORMUL 6 CD 4(CD 2+) FORMUL 10 HOH *422(H2 O) HELIX 1 1 PRO A 2 ASP A 5 5 4 HELIX 2 2 SER A 62 THR A 68 1 7 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 B 306 ASN B 314 1 9 HELIX 11 11 ASN B 315 LEU B 322 1 8 HELIX 12 12 ASN B 335 TYR B 342 1 8 HELIX 13 13 MET B 349 SER B 359 1 11 HELIX 14 14 ASN B 376 LEU B 387 1 12 HELIX 15 15 MET B 430 LYS B 435 1 6 HELIX 16 16 LYS B 435 ASN B 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 BA10 ARG B 396 TYR B 402 0 SHEET 2 BA10 GLY B 406 PHE B 416 -1 O GLY B 406 N TYR B 402 SHEET 3 BA10 ILE B 419 ILE B 424 -1 O ILE B 419 N PHE B 416 SHEET 4 BA10 GLN B 363 GLY B 369 1 O ILE B 364 N ALA B 420 SHEET 5 BA10 LEU A 171 GLY A 177 1 O GLN A 172 N GLN B 363 SHEET 6 BA10 LEU A 144 GLU A 149 1 O LEU A 144 N GLN A 172 SHEET 7 BA10 VAL A 50 LEU A 54 1 O VAL A 50 N PHE A 145 SHEET 8 BA10 ASN A 94 LEU A 98 1 O ASN A 94 N VAL A 51 SHEET 9 BA10 LYS A 32 VAL A 39 -1 O TRP A 37 N TYR A 97 SHEET 10 BA10 TYR A 108 SER A 109 1 O TYR A 108 N HIS A 33 SHEET 1 BB10 ARG B 396 TYR B 402 0 SHEET 2 BB10 GLY B 406 PHE B 416 -1 O GLY B 406 N TYR B 402 SHEET 3 BB10 ILE B 419 ILE B 424 -1 O ILE B 419 N PHE B 416 SHEET 4 BB10 GLN B 363 GLY B 369 1 O ILE B 364 N ALA B 420 SHEET 5 BB10 LEU A 171 GLY A 177 1 O GLN A 172 N GLN B 363 SHEET 6 BB10 LEU A 144 GLU A 149 1 O LEU A 144 N GLN A 172 SHEET 7 BB10 VAL A 50 LEU A 54 1 O VAL A 50 N PHE A 145 SHEET 8 BB10 ASN A 94 LEU A 98 1 O ASN A 94 N VAL A 51 SHEET 9 BB10 LYS A 32 VAL A 39 -1 O TRP A 37 N TYR A 97 SHEET 10 BB10 GLN A 21 LYS A 27 -1 O TYR A 22 N PHE A 38 SHEET 1 AC 2 PHE A 73 VAL A 75 0 SHEET 2 AC 2 LEU A 82 TYR A 84 -1 O GLU A 83 N LEU A 74 SHEET 1 AD 2 CYS A 213 SER A 214 0 SHEET 2 AD 2 LYS A 217 CYS A 218 -1 O LYS A 217 N SER A 214 SSBOND 1 CYS A 60 CYS B 334 1555 1555 2.04 SSBOND 2 CYS A 212 CYS A 228 1555 1555 2.03 SSBOND 3 CYS A 213 CYS A 218 1555 1555 2.03 SSBOND 4 CYS A 253 CYS B 303 1555 1555 2.03 LINK ND2 ASN A 117 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN B 305 C1 NAG D 1 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.42 LINK OD2 ASP A 3 CD CD A1261 3455 1555 2.28 LINK OD1 ASP A 3 CD CD A1261 3455 1555 2.43 LINK OE2 GLU A 184 CD CD A1260 1555 1555 2.77 LINK OE1 GLU A 184 CD CD A1260 1555 1555 3.01 LINK ND1 HIS A 211 CD CD A1261 1555 1555 2.20 LINK OD2 ASP A 222 CD CD A1262 1555 1555 2.76 LINK OD1 ASP A 222 CD CD A1262 1555 1555 2.38 LINK OD1 ASP A 225 CD CD A1261 1555 1555 2.70 LINK OD2 ASP A 225 CD CD A1261 1555 1555 2.28 LINK CD CD A1261 O HOH A2220 1555 1555 2.44 LINK CD CD A1262 OE2 GLU B 326 1555 4456 2.45 LINK CD CD A1262 OE1 GLU B 326 1555 4456 3.04 LINK O ALA B 374 CD CD B1454 1555 1555 2.78 LINK SG CYS B 375 CD CD B1454 1555 1555 1.99 LINK CD CD B1454 O HOH B2091 1555 1555 2.37 CISPEP 1 GLY A 57 PRO A 58 0 -3.03 CISPEP 2 SER A 100 PRO A 101 0 -1.28 CRYST1 90.590 102.800 48.390 90.00 101.87 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 0.011039 0.000000 0.002320 0.00000 SCALE2 0.000000 0.009728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021117 0.00000