PDB Short entry for 3K9M HEADER HYDROLASE/HYDROLASE INHIBITOR 16-OCT-09 3K9M TITLE CATHEPSIN B IN COMPLEX WITH STEFIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CATHEPSIN B1, APP SECRETASE, APPS, CATHEPSIN B LIGHT CHAIN, COMPND 5 CATHEPSIN B HEAVY CHAIN; COMPND 6 EC: 3.4.22.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CYSTATIN-A; COMPND 10 CHAIN: C, D; COMPND 11 SYNONYM: CYSTATIN-AS, STEFIN-A; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CTSB, CPSB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CSTA, STF1, STFA; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS DISULFIDE BOND, GLYCOPROTEIN, LYSOSOME, PROTEASE, THIOL PROTEASE, KEYWDS 2 ZYMOGEN, THIOL PROTEASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.RENKO,D.TURK REVDAT 3 01-NOV-17 3K9M 1 REMARK REVDAT 2 05-OCT-11 3K9M 1 JRNL VERSN HEADER KEYWDS REVDAT 1 03-NOV-09 3K9M 0 JRNL AUTH M.RENKO,U.POZGAN,D.MAJERA,D.TURK JRNL TITL STEFIN A DISPLACES THE OCCLUDING LOOP OF CATHEPSIN B ONLY BY JRNL TITL 2 AS MUCH AS REQUIRED TO BIND TO THE ACTIVE SITE CLEFT JRNL REF FEBS J. V. 277 4338 2010 JRNL REFN ISSN 1742-464X JRNL PMID 20860624 JRNL DOI 10.1111/J.1742-4658.2010.07824.X REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 14360 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 713 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) : 2.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 711 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5454 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.46000 REMARK 3 B22 (A**2) : 4.54000 REMARK 3 B33 (A**2) : -3.22000 REMARK 3 B12 (A**2) : -1.31000 REMARK 3 B13 (A**2) : -4.29000 REMARK 3 B23 (A**2) : -1.65000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.343 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5506 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7484 ; 1.709 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 689 ; 7.197 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 250 ;38.572 ;24.720 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 851 ;22.513 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;24.331 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 773 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4290 ; 0.009 ; 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): 3437 ; 0.790 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5514 ; 1.478 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2069 ; 1.586 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1970 ; 2.723 ; 4.500 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: THE STRUCTURE WAS REFINED ALSO WITH REMARK 3 MAIN REMARK 4 REMARK 4 3K9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99988 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI111 REMARK 200 OPTICS : DOUBLE CRYSTAL SI111 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.20600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1NB3 AND 1SP4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SUPHATE, 24% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 REMARK 350 BIOMOLECULE: 2 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: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLU A 95 REMARK 475 VAL A 112 REMARK 475 ASN A 113 REMARK 475 GLY A 114 REMARK 475 SER A 115 REMARK 475 MET C 1 REMARK 475 ASP B 254 REMARK 475 GLU D 78 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 86 CD CE NZ REMARK 480 SER A 96 CB OG REMARK 480 ILE A 105 CB CG1 CD1 REMARK 480 GLU A 122 CG CD OE1 OE2 REMARK 480 LYS A 158 CD CE NZ REMARK 480 GLN C 76 CG CD OE1 NE2 REMARK 480 LYS B 86 CD CE NZ REMARK 480 LYS B 127 CE NZ REMARK 480 LYS B 158 CD CE NZ REMARK 480 GLU D 18 CG CD OE1 OE2 REMARK 480 LYS D 22 CD CE NZ REMARK 480 LYS D 30 CG CD CE NZ REMARK 480 ASP D 61 OD1 OD2 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 NZ LYS C 44 O LEU C 95 2.10 REMARK 500 OE2 GLU A 194 NZ LYS C 10 2.12 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 PRO A 134 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 LEU B 1 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 PRO D 3 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 PRO D 3 C - N - CD ANGL. DEV. = -16.3 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 ALA A 48 -2.31 89.80 REMARK 500 ALA A 77 -8.50 -59.65 REMARK 500 VAL A 89 -159.48 -79.34 REMARK 500 GLU A 95 26.71 118.81 REMARK 500 SER A 96 -78.72 82.25 REMARK 500 HIS A 97 -101.75 -6.26 REMARK 500 VAL A 98 148.71 177.51 REMARK 500 ARG A 101 79.87 -118.35 REMARK 500 HIS A 110 -47.45 132.90 REMARK 500 HIS A 111 -63.61 108.14 REMARK 500 VAL A 112 -179.29 26.37 REMARK 500 ASN A 113 -86.66 66.83 REMARK 500 SER A 115 118.19 68.27 REMARK 500 ARG A 116 105.46 -33.75 REMARK 500 PRO A 117 38.66 -145.62 REMARK 500 CYS A 119 -100.52 -67.35 REMARK 500 THR A 120 62.82 21.01 REMARK 500 ASP A 124 100.69 -161.03 REMARK 500 THR A 125 115.22 -29.34 REMARK 500 PRO A 134 146.01 -30.59 REMARK 500 PRO A 138 -132.47 -94.20 REMARK 500 ASN A 155 81.79 -68.49 REMARK 500 PRO A 169 157.20 -40.52 REMARK 500 SER A 178 -35.93 -35.59 REMARK 500 LYS A 184 -57.73 -133.42 REMARK 500 THR A 192 -121.10 -142.90 REMARK 500 ASN A 210 -100.89 44.58 REMARK 500 ASN A 222 178.06 82.70 REMARK 500 ASP A 227 72.21 -112.10 REMARK 500 ASP A 238 37.73 76.00 REMARK 500 THR A 253 -50.55 89.71 REMARK 500 ILE C 2 106.03 -45.98 REMARK 500 PRO C 3 49.68 -76.66 REMARK 500 ASN C 32 -4.32 71.41 REMARK 500 LYS C 37 126.85 177.55 REMARK 500 VAL C 48 -167.43 -122.64 REMARK 500 ALA C 59 -109.32 -99.18 REMARK 500 ASP C 61 -138.91 -82.51 REMARK 500 ASN C 62 70.43 -109.70 REMARK 500 SER C 72 177.99 -58.77 REMARK 500 ASN C 77 175.40 147.44 REMARK 500 ASP C 79 -141.50 -103.21 REMARK 500 LEU C 80 144.27 148.45 REMARK 500 VAL C 81 130.90 -176.16 REMARK 500 GLN C 86 60.06 -165.77 REMARK 500 ASP C 88 62.06 62.14 REMARK 500 SER B 28 12.55 -64.45 REMARK 500 CYS B 71 1.65 -67.56 REMARK 500 ARG B 85 -75.31 -87.95 REMARK 500 VAL B 89 -153.62 -94.47 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1STF RELATED DB: PDB REMARK 900 PAPAIN IN COMPLEX WITH STEFIN B REMARK 900 RELATED ID: 1NB3 RELATED DB: PDB REMARK 900 CATHEPSIN H (PAPAIN LIKE PROTEASE) IN COMPLEX WITH STEFIN A DBREF 3K9M A 1 254 UNP P07858 CATB_HUMAN 80 333 DBREF 3K9M C 1 98 UNP P01040 CYTA_HUMAN 1 98 DBREF 3K9M B 1 254 UNP P07858 CATB_HUMAN 80 333 DBREF 3K9M D 1 98 UNP P01040 CYTA_HUMAN 1 98 SEQRES 1 A 254 LEU PRO ALA SER PHE ASP ALA ARG GLU GLN TRP PRO GLN SEQRES 2 A 254 CYS PRO THR ILE LYS GLU ILE ARG ASP GLN GLY SER CYS SEQRES 3 A 254 GLY SER CYS TRP ALA PHE GLY ALA VAL GLU ALA ILE SER SEQRES 4 A 254 ASP ARG ILE CYS ILE HIS THR ASN ALA HIS VAL SER VAL SEQRES 5 A 254 GLU VAL SER ALA GLU ASP LEU LEU THR CYS CYS GLY SER SEQRES 6 A 254 MET CYS GLY ASP GLY CYS ASN GLY GLY TYR PRO ALA GLU SEQRES 7 A 254 ALA TRP ASN PHE TRP THR ARG LYS GLY LEU VAL SER GLY SEQRES 8 A 254 GLY LEU TYR GLU SER HIS VAL GLY CYS ARG PRO TYR SER SEQRES 9 A 254 ILE PRO PRO CYS GLU HIS HIS VAL ASN GLY SER ARG PRO SEQRES 10 A 254 PRO CYS THR GLY GLU GLY ASP THR PRO LYS CYS SER LYS SEQRES 11 A 254 ILE CYS GLU PRO GLY TYR SER PRO THR TYR LYS GLN ASP SEQRES 12 A 254 LYS HIS TYR GLY TYR ASN SER TYR SER VAL SER ASN SER SEQRES 13 A 254 GLU LYS ASP ILE MET ALA GLU ILE TYR LYS ASN GLY PRO SEQRES 14 A 254 VAL GLU GLY ALA PHE SER VAL TYR SER ASP PHE LEU LEU SEQRES 15 A 254 TYR LYS SER GLY VAL TYR GLN HIS VAL THR GLY GLU MET SEQRES 16 A 254 MET GLY GLY HIS ALA ILE ARG ILE LEU GLY TRP GLY VAL SEQRES 17 A 254 GLU ASN GLY THR PRO TYR TRP LEU VAL ALA ASN SER TRP SEQRES 18 A 254 ASN THR ASP TRP GLY ASP ASN GLY PHE PHE LYS ILE LEU SEQRES 19 A 254 ARG GLY GLN ASP HIS CYS GLY ILE GLU SER GLU VAL VAL SEQRES 20 A 254 ALA GLY ILE PRO ARG THR ASP SEQRES 1 C 98 MET ILE PRO GLY GLY LEU SER GLU ALA LYS PRO ALA THR SEQRES 2 C 98 PRO GLU ILE GLN GLU ILE VAL ASP LYS VAL LYS PRO GLN SEQRES 3 C 98 LEU GLU GLU LYS THR ASN GLU THR TYR GLY LYS LEU GLU SEQRES 4 C 98 ALA VAL GLN TYR LYS THR GLN VAL VAL ALA GLY THR ASN SEQRES 5 C 98 TYR TYR ILE LYS VAL ARG ALA GLY ASP ASN LYS TYR MET SEQRES 6 C 98 HIS LEU LYS VAL PHE LYS SER LEU PRO GLY GLN ASN GLU SEQRES 7 C 98 ASP LEU VAL LEU THR GLY TYR GLN VAL ASP LYS ASN LYS SEQRES 8 C 98 ASP ASP GLU LEU THR GLY PHE SEQRES 1 B 254 LEU PRO ALA SER PHE ASP ALA ARG GLU GLN TRP PRO GLN SEQRES 2 B 254 CYS PRO THR ILE LYS GLU ILE ARG ASP GLN GLY SER CYS SEQRES 3 B 254 GLY SER CYS TRP ALA PHE GLY ALA VAL GLU ALA ILE SER SEQRES 4 B 254 ASP ARG ILE CYS ILE HIS THR ASN ALA HIS VAL SER VAL SEQRES 5 B 254 GLU VAL SER ALA GLU ASP LEU LEU THR CYS CYS GLY SER SEQRES 6 B 254 MET CYS GLY ASP GLY CYS ASN GLY GLY TYR PRO ALA GLU SEQRES 7 B 254 ALA TRP ASN PHE TRP THR ARG LYS GLY LEU VAL SER GLY SEQRES 8 B 254 GLY LEU TYR GLU SER HIS VAL GLY CYS ARG PRO TYR SER SEQRES 9 B 254 ILE PRO PRO CYS GLU HIS HIS VAL ASN GLY SER ARG PRO SEQRES 10 B 254 PRO CYS THR GLY GLU GLY ASP THR PRO LYS CYS SER LYS SEQRES 11 B 254 ILE CYS GLU PRO GLY TYR SER PRO THR TYR LYS GLN ASP SEQRES 12 B 254 LYS HIS TYR GLY TYR ASN SER TYR SER VAL SER ASN SER SEQRES 13 B 254 GLU LYS ASP ILE MET ALA GLU ILE TYR LYS ASN GLY PRO SEQRES 14 B 254 VAL GLU GLY ALA PHE SER VAL TYR SER ASP PHE LEU LEU SEQRES 15 B 254 TYR LYS SER GLY VAL TYR GLN HIS VAL THR GLY GLU MET SEQRES 16 B 254 MET GLY GLY HIS ALA ILE ARG ILE LEU GLY TRP GLY VAL SEQRES 17 B 254 GLU ASN GLY THR PRO TYR TRP LEU VAL ALA ASN SER TRP SEQRES 18 B 254 ASN THR ASP TRP GLY ASP ASN GLY PHE PHE LYS ILE LEU SEQRES 19 B 254 ARG GLY GLN ASP HIS CYS GLY ILE GLU SER GLU VAL VAL SEQRES 20 B 254 ALA GLY ILE PRO ARG THR ASP SEQRES 1 D 98 MET ILE PRO GLY GLY LEU SER GLU ALA LYS PRO ALA THR SEQRES 2 D 98 PRO GLU ILE GLN GLU ILE VAL ASP LYS VAL LYS PRO GLN SEQRES 3 D 98 LEU GLU GLU LYS THR ASN GLU THR TYR GLY LYS LEU GLU SEQRES 4 D 98 ALA VAL GLN TYR LYS THR GLN VAL VAL ALA GLY THR ASN SEQRES 5 D 98 TYR TYR ILE LYS VAL ARG ALA GLY ASP ASN LYS TYR MET SEQRES 6 D 98 HIS LEU LYS VAL PHE LYS SER LEU PRO GLY GLN ASN GLU SEQRES 7 D 98 ASP LEU VAL LEU THR GLY TYR GLN VAL ASP LYS ASN LYS SEQRES 8 D 98 ASP ASP GLU LEU THR GLY PHE FORMUL 5 HOH *127(H2 O) HELIX 1 1 ALA A 7 TRP A 11 1 5 HELIX 2 2 CYS A 14 GLU A 19 5 6 HELIX 3 3 SER A 28 THR A 46 1 19 HELIX 4 4 SER A 55 CYS A 63 1 9 HELIX 5 5 GLY A 64 GLY A 68 5 5 HELIX 6 6 ASP A 69 GLY A 73 5 5 HELIX 7 7 TYR A 75 LYS A 86 1 12 HELIX 8 8 THR A 139 LYS A 144 1 6 HELIX 9 9 SER A 156 GLY A 168 1 13 HELIX 10 10 ASP A 179 LEU A 181 5 3 HELIX 11 11 THR C 13 VAL C 23 1 11 HELIX 12 12 VAL C 23 ASN C 32 1 10 HELIX 13 13 ALA B 7 TRP B 11 1 5 HELIX 14 14 CYS B 14 LYS B 18 5 5 HELIX 15 15 SER B 28 HIS B 45 1 18 HELIX 16 16 SER B 55 GLY B 64 1 10 HELIX 17 17 SER B 65 GLY B 68 5 4 HELIX 18 18 ASP B 69 GLY B 73 5 5 HELIX 19 19 TYR B 75 LYS B 86 1 12 HELIX 20 20 HIS B 111 SER B 115 5 5 HELIX 21 21 THR B 139 LYS B 144 1 6 HELIX 22 22 SER B 156 GLY B 168 1 13 HELIX 23 23 ASP B 179 TYR B 183 5 5 HELIX 24 24 ASP B 238 ILE B 242 5 5 HELIX 25 25 THR D 13 ASN D 32 1 20 SHEET 1 A 3 PHE A 5 ASP A 6 0 SHEET 2 A 3 MET A 195 GLU A 209 -1 O TRP A 206 N PHE A 5 SHEET 3 A 3 VAL A 170 TYR A 177 -1 N VAL A 170 O ILE A 203 SHEET 1 B 4 PHE A 5 ASP A 6 0 SHEET 2 B 4 MET A 195 GLU A 209 -1 O TRP A 206 N PHE A 5 SHEET 3 B 4 THR A 212 ALA A 218 -1 O TYR A 214 N GLY A 207 SHEET 4 B 4 PHE A 230 LEU A 234 -1 O PHE A 231 N VAL A 217 SHEET 1 C 2 VAL A 52 VAL A 54 0 SHEET 2 C 2 SER A 90 LEU A 93 -1 O GLY A 92 N GLU A 53 SHEET 1 D 2 GLY A 147 SER A 152 0 SHEET 2 D 2 VAL A 247 PRO A 251 -1 O ILE A 250 N TYR A 148 SHEET 1 E 5 LYS C 10 PRO C 11 0 SHEET 2 E 5 GLU C 39 VAL C 47 -1 O TYR C 43 N LYS C 10 SHEET 3 E 5 THR C 51 ARG C 58 -1 O TYR C 54 N LYS C 44 SHEET 4 E 5 TYR C 64 LYS C 71 -1 O MET C 65 N VAL C 57 SHEET 5 E 5 VAL C 81 GLN C 86 -1 O GLY C 84 N LYS C 68 SHEET 1 F 3 PHE B 5 ASP B 6 0 SHEET 2 F 3 MET B 195 GLU B 209 -1 O TRP B 206 N PHE B 5 SHEET 3 F 3 VAL B 170 TYR B 177 -1 N VAL B 176 O MET B 196 SHEET 1 G 5 PHE B 5 ASP B 6 0 SHEET 2 G 5 MET B 195 GLU B 209 -1 O TRP B 206 N PHE B 5 SHEET 3 G 5 THR B 212 ALA B 218 -1 O ALA B 218 N ARG B 202 SHEET 4 G 5 PHE B 230 LEU B 234 -1 O PHE B 231 N VAL B 217 SHEET 5 G 5 VAL B 187 TYR B 188 1 N TYR B 188 O LYS B 232 SHEET 1 H 3 VAL B 52 VAL B 54 0 SHEET 2 H 3 SER B 90 LEU B 93 -1 O GLY B 91 N GLU B 53 SHEET 3 H 3 HIS B 97 VAL B 98 -1 O HIS B 97 N LEU B 93 SHEET 1 I 2 GLY B 147 SER B 152 0 SHEET 2 I 2 VAL B 247 PRO B 251 -1 O ILE B 250 N TYR B 148 SHEET 1 J 5 LYS D 10 PRO D 11 0 SHEET 2 J 5 ALA D 40 VAL D 47 -1 O TYR D 43 N LYS D 10 SHEET 3 J 5 THR D 51 VAL D 57 -1 O TYR D 54 N LYS D 44 SHEET 4 J 5 MET D 65 LYS D 71 -1 O LYS D 71 N THR D 51 SHEET 5 J 5 VAL D 81 LEU D 82 -1 O VAL D 81 N PHE D 70 SSBOND 1 CYS A 14 CYS A 43 1555 1555 2.06 SSBOND 2 CYS A 26 CYS A 71 1555 1555 2.02 SSBOND 3 CYS A 62 CYS A 128 1555 1555 2.05 SSBOND 4 CYS A 63 CYS A 67 1555 1555 2.02 SSBOND 5 CYS A 100 CYS A 132 1555 1555 2.04 SSBOND 6 CYS A 108 CYS A 119 1555 1555 2.02 SSBOND 7 CYS B 14 CYS B 43 1555 1555 2.07 SSBOND 8 CYS B 26 CYS B 71 1555 1555 2.02 SSBOND 9 CYS B 62 CYS B 128 1555 1555 2.04 SSBOND 10 CYS B 63 CYS B 67 1555 1555 2.02 SSBOND 11 CYS B 100 CYS B 132 1555 1555 2.02 SSBOND 12 CYS B 108 CYS B 119 1555 1555 2.03 CISPEP 1 SER A 137 PRO A 138 0 3.41 CISPEP 2 SER B 137 PRO B 138 0 2.21 CRYST1 62.122 31.078 70.937 89.95 104.45 89.90 P 1 2 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 0.016097 -0.000029 0.004149 0.00000 SCALE2 0.000000 0.032177 -0.000044 0.00000 SCALE3 0.000000 0.000000 0.014558 0.00000