| content |
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 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
JRNL TITL 2 CATHEPSIN 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,SMART,VONRHEIN,WOMACK,
REMARK 3 : 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)) : 0.0
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.05
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 (%) : 4.91
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 : 3302
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 130
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) : -0.5078
REMARK 3 B22 (A**2) : -0.5904
REMARK 3 B33 (A**2) : 1.0981
REMARK 3 B12 (A**2) : 0.0000
REMARK 3 B13 (A**2) : 0.1075
REMARK 3 B23 (A**2) : 0.0000
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 : 0.9447
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.9265
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 3533 ; 2.00 ; HARMONIC
REMARK 3 BOND ANGLES : 4823 ; 2.00 ; HARMONIC
REMARK 3 TORSION ANGLES : 1183 ; 2.00 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 95 ; 2.00 ; HARMONIC
REMARK 3 GENERAL PLANES : 507 ; 5.00 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 3533 ; 20.00 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.00 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 436 ; 5.00 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 3 ; 1.00 ; 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 ; 4.00 ; 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 DEFAULT
REMARK 3 CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED 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 24-JUL-12.
REMARK 100 THE PDBE ID CODE IS EBI-53025.
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 (QUANTUM 315R)
REMARK 200 DETECTOR MANUFACTURER : ADSC
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) : 2.04
REMARK 200 RESOLUTION RANGE LOW (A) : 67.10
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 200 DATA REDUNDANCY : 3.7
REMARK 200 R MERGE (I) : 0.06
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 14.90
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 : 3.7
REMARK 200 R MERGE FOR SHELL (I) : 0.35
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 4.00
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 (%): 48.7
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.4
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CATA WAS CRYSTALLIZED USING THE
REMARK 280 HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING
REMARK 280 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM
REMARK 280 NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING
REMARK 280 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2,
REMARK 280 AND SET TO EQUILIBRATE AT 4 DEG. C. ROD-SHAPED CRYSTALS
REMARK 280 APPEARED IN ABOUT ONE WEEK.
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
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
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 B2151 DISTANCE = 7.46 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 A1260 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 184 OE1
REMARK 620 2 GLU A 184 OE2 44.5
REMARK 620 N 1
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 HIS A 211 ND1
REMARK 620 2 ASP A 3 OD2 112.5
REMARK 620 3 HOH A2220 O 97.1 137.3
REMARK 620 4 ASP A 3 OD1 86.9 56.0 97.8
REMARK 620 5 ASP A 225 OD1 95.9 72.5 136.1 124.6
REMARK 620 6 ASP A 225 OD2 135.7 87.7 91.9 134.6 51.5
REMARK 620 N 1 2 3 4 5
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 GLU B 326 OE1
REMARK 620 2 ASP A 222 OD1 166.0
REMARK 620 3 ASP A 222 OD2 122.2 49.9
REMARK 620 4 GLU B 326 OE2 45.7 120.3 90.0
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 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B1454
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN A OF SUGAR BOUND TO
REMARK 800 ASN A 117 RESIDUES 3010 TO 3011
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
HET NAG A3010 14
HET NAG A3011 14
HET NAG A3020 14
HET NAG A3021 14
HET S35 A1259 70
HET CD A1260 1
HET CD A1261 1
HET CD A1262 1
HET CD B1454 1
HETNAM S35 (3S)-3-({[1-(2-FLUOROPHENYL)-5-{[(2R)-2-
HETNAM 2 S35 HYDROXY-3,3-DIMETHYLBUTYL]OXY}-1H-PYRAZOL-3-YL]
HETNAM 3 S35 CARBONYL}AMINO)-3-(2-METHYLPHENYL)PROPANOIC
HETNAM 4 S35 ACID
HETNAM CD CADMIUM ION
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 3 S35 C26 H30 F N3 O5
FORMUL 4 CD 4(CD 2+)
FORMUL 5 NAG 4(C8 H15 N O6)
FORMUL 6 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 A3010 1555 1555 1.43
LINK CD CD A1260 OE2 GLU A 184 1555 1555 2.77
LINK CD CD A1260 OE1 GLU A 184 1555 1555 3.01
LINK CD CD A1261 OD2 ASP A 3 1555 3455 2.28
LINK CD CD A1261 O HOH A2220 1555 1555 2.44
LINK CD CD A1261 OD1 ASP A 3 1555 3455 2.43
LINK CD CD A1261 OD1 ASP A 225 1555 1555 2.70
LINK CD CD A1261 OD2 ASP A 225 1555 1555 2.28
LINK CD CD A1261 ND1 HIS A 211 1555 1555 2.20
LINK CD CD A1262 OD2 ASP A 222 1555 1555 2.76
LINK CD CD A1262 OE2 GLU B 326 1555 4456 2.45
LINK CD CD A1262 OD1 ASP A 222 1555 1555 2.38
LINK CD CD A1262 OE1 GLU B 326 1555 4456 3.04
LINK O4 NAG A3010 C1 NAG A3011 1555 1555 1.43
LINK O4 NAG A3020 C1 NAG A3021 1555 1555 1.42
LINK ND2 ASN B 305 C1 NAG A3020 1555 1555 1.43
LINK CD CD B1454 O HOH B2091 1555 1555 2.37
LINK CD CD B1454 SG CYS B 375 1555 1555 1.99
LINK CD CD B1454 O ALA B 374 1555 1555 2.78
CISPEP 1 GLY A 57 PRO A 58 0 -3.03
CISPEP 2 SER A 100 PRO A 101 0 -1.28
SITE 1 AC1 5 LEU A 180 ASN A 186 ALA B 374 CYS B 375
SITE 2 AC1 5 HOH B2091
SITE 1 AC2 8 ASN A 117 GLU A 120 HOH A2137 HOH A2259
SITE 2 AC2 8 HOH A2260 HOH A2261 HOH A2262 ARG B 343
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
TER 2020 PRO A 258
TER 3304 GLU B 453
MASTER 386 0 9 16 28 0 4 6 3854 2 151 36
END |