HEADER HYDROLASE 06-DEC-13 4CI9 TITLE CRYSTAL STRUCTURE OF CATHEPSIN A, APO-STRUCTURE 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, DRUG DISCOVERY, SERINE CARBOXYPEPTIDASE, CARDIOVASCULAR KEYWDS 2 DRUG, HEART FAILURE, ENDOTHELIN, TETRAHEDRAL INTERMEDIATE, COVALENT KEYWDS 3 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 4CI9 1 HETSYN REVDAT 4 29-JUL-20 4CI9 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-MAR-19 4CI9 1 JRNL REMARK LINK REVDAT 2 02-APR-14 4CI9 1 JRNL REVDAT 1 26-FEB-14 4CI9 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. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 56890 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2843 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.62 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.52 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3982 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2204 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3780 REMARK 3 BIN R VALUE (WORKING SET) : 0.2196 REMARK 3 BIN FREE R VALUE : 0.2340 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 202 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 : 3302 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 614 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.12150 REMARK 3 B22 (A**2) : 0.30080 REMARK 3 B33 (A**2) : -3.42230 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.47780 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.165 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.089 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.085 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.083 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.081 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 : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3576 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4882 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1213 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 99 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 520 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3576 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 441 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 12 ; 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 : 4641 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.84 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.59 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4CI9 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_1290059176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-12 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56973 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 33.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 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 45.15500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.15500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.01500 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: 8430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 -1.000000 0.000000 0.000000 -90.31000 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 A2130 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2350 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2385 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 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 MET A 299 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 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 -75.21 -109.15 REMARK 500 SER A 150 -114.45 56.79 REMARK 500 SER A 150 -109.91 53.80 REMARK 500 GLN A 215 -120.52 64.64 REMARK 500 TYR A 221 -66.26 -97.95 REMARK 500 ASN A 248 97.10 -165.96 REMARK 500 TYR A 402 59.34 -100.01 REMARK 500 MET A 430 79.16 -107.59 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 A2019 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A2020 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH A2083 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A2086 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A2087 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A2100 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A2180 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A2230 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A2233 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A2250 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A2591 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2611 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH A2612 DISTANCE = 8.94 ANGSTROMS REMARK 525 HOH A2613 DISTANCE = 8.19 ANGSTROMS REMARK 525 HOH A2614 DISTANCE = 6.45 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DMS A 1454 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CIA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATHEPSIN A, COMPLEXED WITH COMPOUND 1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AT THE C-TERMINUS, ONE EXTRA GLU IS PRESENT AS A LEFTOVER REMARK 999 FROM A MYC-TAG DBREF 4CI9 A 1 452 UNP P10619 PPGB_HUMAN 29 480 SEQADV 4CI9 SER A -1 UNP P10619 EXPRESSION TAG SEQADV 4CI9 ARG A 0 UNP P10619 EXPRESSION TAG SEQADV 4CI9 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 4CI9 ASN A 117 ASN GLYCOSYLATION SITE MODRES 4CI9 ASN A 305 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET DMS A1454 3 HET ACT A1455 4 HET ACT A1456 4 HET GOL A1457 6 HET GOL A1458 6 HET SO4 A1459 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM DMS DIMETHYL SULFOXIDE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 4 DMS C2 H6 O S FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *614(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 GLN A 165 1 15 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 GLY A 403 SER A 405 5 3 HELIX 16 16 MET A 430 LYS A 435 1 6 HELIX 17 17 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 2.04 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 A 303 1555 1555 2.04 LINK ND2 ASN A 117 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 305 C1 NAG C 1 1555 1555 1.43 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.42 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.42 CISPEP 1 GLY A 57 PRO A 58 0 -2.06 CISPEP 2 SER A 100 PRO A 101 0 -1.58 CRYST1 90.310 102.030 48.550 90.00 101.27 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 0.011073 0.000000 0.002207 0.00000 SCALE2 0.000000 0.009801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021002 0.00000