PDB Short entry for 1PPP HEADER HYDROLASE(SULFHYDRYL PROTEINASE) 17-MAR-93 1PPP TITLE CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TITLE 2 TO PAPAIN S2 AND S3 SUBSITES CAVEAT 1PPP CHIRALITY ERROR AT CB IN RESIDUES 1 AND 125 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649 KEYWDS HYDROLASE(SULFHYDRYL PROTEINASE) EXPDTA X-RAY DIFFRACTION AUTHOR T.ISHIDA REVDAT 5 09-MAY-12 1PPP 1 COMPND VERSN REVDAT 4 25-AUG-09 1PPP 1 SOURCE REVDAT 3 24-FEB-09 1PPP 1 VERSN REVDAT 2 01-APR-03 1PPP 1 JRNL REVDAT 1 31-JAN-94 1PPP 0 JRNL AUTH M.J.KIM,D.YAMAMOTO,K.MATSUMOTO,M.INOUE,T.ISHIDA,H.MIZUNO, JRNL AUTH 2 S.SUMIYA,K.KITAMURA JRNL TITL CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY JRNL TITL 2 OF E64-C TO PAPAIN S2 AND S3 SUBSITES. JRNL REF BIOCHEM.J. V. 287 797 1992 JRNL REFN ISSN 0264-6021 JRNL PMID 1445241 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.YAMAMOTO,K.MATSUMOTO,H.OHISHI,T.ISHIDA,M.INOUE,K.KITAMURA, REMARK 1 AUTH 2 H.MIZUNO REMARK 1 TITL REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT REMARK 1 TITL 2 2.1-ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 266 14771 1991 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.MATSUMOTO,D.YAMAMOTO,H.OHISHI,K.TOMOO,T.ISHIDA,M.INOUE, REMARK 1 AUTH 2 T.SADATOME,K.KITAMURA,H.MIZUNO REMARK 1 TITL MODE OF BINDING OF E-64-C, A POTENT THIOL PROTEASE REMARK 1 TITL 2 INHIBITOR, TO PAPAIN AS DETERMINED BY X-RAY CRYSTAL ANALYSIS REMARK 1 TITL 3 OF THE COMPLEX REMARK 1 REF FEBS LETT. V. 245 171 1989 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.YAMAMOTO,K.MATSUMOTO,H.OHISHI,T.ISHIDA,M.INOUE,K.KITAMURA, REMARK 1 AUTH 2 H.MIZUNO REMARK 1 TITL THE IMPORTANCE OF VAL-157 HYDROPHOBIC INTERACTION FOR PAPAIN REMARK 1 TITL 2 INHIBITORY ACTIVITY OF AN EPOXYSUCCINYL AMINO ACID REMARK 1 TITL 3 DERIVATIVE; A STRUCTURE-ACTIVITY RELATIONSHIP BASED ON THE REMARK 1 TITL 4 CRYSTAL STRUCTURE OF THE PAPAIN-E-64-C COMPLEX REMARK 1 REF FEBS LETT. V. 253 134 1990 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.049 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.68500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.97500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.97500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.68500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.17000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS A 106 NZ LYS A 211 2.07 REMARK 500 NH2 ARG A 58 O HOH A 357 2.17 REMARK 500 O GLY A 201 OG1 THR A 204 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 242 O HOH A 307 1655 1.69 REMARK 500 OH TYR A 94 O HOH A 275 4456 1.78 REMARK 500 O HOH A 253 O HOH A 370 2865 1.94 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 ILE A 1 CB - CA - C ANGL. DEV. = 14.6 DEGREES REMARK 500 ASP A 6 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 TYR A 48 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 59 CB - CA - C ANGL. DEV. = 13.7 DEGREES REMARK 500 ARG A 59 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 59 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 59 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 59 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLY A 65 N - CA - C ANGL. DEV. = 18.0 DEGREES REMARK 500 GLY A 65 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 TYR A 67 CB - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TYR A 67 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 83 CD - NE - CZ ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG A 83 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 TYR A 86 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 TYR A 86 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 VAL A 91 CA - CB - CG1 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 96 NH1 - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 98 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 GLU A 99 CA - CB - CG ANGL. DEV. = 17.6 DEGREES REMARK 500 GLY A 146 CA - C - O ANGL. DEV. = -15.7 DEGREES REMARK 500 GLY A 147 N - CA - C ANGL. DEV. = 20.5 DEGREES REMARK 500 GLY A 146 CA - C - N ANGL. DEV. = 16.6 DEGREES REMARK 500 ASP A 158 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 ASP A 158 CB - CG - OD1 ANGL. DEV. = 13.7 DEGREES REMARK 500 ASP A 158 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 TRP A 177 CA - C - N ANGL. DEV. = 13.6 DEGREES REMARK 500 GLU A 183 OE1 - CD - OE2 ANGL. DEV. = -9.0 DEGREES REMARK 500 GLU A 183 CG - CD - OE1 ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 TYR A 203 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 203 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 SER A 205 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 SER A 206 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 TYR A 208 CB - CG - CD2 ANGL. DEV. = 4.7 DEGREES REMARK 500 TYR A 208 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 21 25.79 -76.96 REMARK 500 ASN A 64 43.58 80.23 REMARK 500 TYR A 78 -93.51 -96.96 REMARK 500 GLN A 128 158.81 176.09 REMARK 500 ARG A 145 18.75 -142.25 REMARK 500 ASP A 158 9.80 -153.63 REMARK 500 SER A 205 100.61 -166.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 145 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 1 47.3 L L OUTSIDE RANGE REMARK 500 LYS A 100 24.1 L L OUTSIDE RANGE REMARK 500 ILE A 125 -28.6 S R CBETA WRONG HAND REMARK 500 ILE A 173 -33.2 S R CBETA WRONG HAND 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 A 244 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH A 251 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 262 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH A 265 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH A 266 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 267 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 268 DISTANCE = 5.70 ANGSTROMS REMARK 525 HOH A 269 DISTANCE = 7.34 ANGSTROMS REMARK 525 HOH A 270 DISTANCE = 11.73 ANGSTROMS REMARK 525 HOH A 271 DISTANCE = 10.67 ANGSTROMS REMARK 525 HOH A 272 DISTANCE = 10.75 ANGSTROMS REMARK 525 HOH A 291 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 292 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH A 293 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A 294 DISTANCE = 7.50 ANGSTROMS REMARK 525 HOH A 296 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 300 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH A 302 DISTANCE = 8.84 ANGSTROMS REMARK 525 HOH A 307 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 316 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH A 318 DISTANCE = 10.19 ANGSTROMS REMARK 525 HOH A 319 DISTANCE = 5.59 ANGSTROMS REMARK 525 HOH A 322 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 324 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 325 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 327 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 328 DISTANCE = 8.88 ANGSTROMS REMARK 525 HOH A 329 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH A 330 DISTANCE = 8.71 ANGSTROMS REMARK 525 HOH A 332 DISTANCE = 5.80 ANGSTROMS REMARK 525 HOH A 336 DISTANCE = 8.32 ANGSTROMS REMARK 525 HOH A 337 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH A 338 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH A 346 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH A 347 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A 352 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 356 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH A 359 DISTANCE = 7.64 ANGSTROMS REMARK 525 HOH A 360 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH A 362 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A 370 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH A 374 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A 388 DISTANCE = 8.65 ANGSTROMS REMARK 525 HOH A 389 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH A 394 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A 400 DISTANCE = 9.39 ANGSTROMS REMARK 525 HOH A 406 DISTANCE = 9.78 ANGSTROMS REMARK 525 HOH A 408 DISTANCE = 11.37 ANGSTROMS REMARK 525 HOH A 410 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH A 411 DISTANCE = 5.54 ANGSTROMS REMARK 525 HOH A 413 DISTANCE = 8.52 ANGSTROMS REMARK 525 HOH A 414 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 415 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A 416 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH A 419 DISTANCE = 5.85 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 E6C IS (2S,3S)-3-(1-(N-(3-METHYLBUTYL)AMINO)- REMARK 600 LEUCYLCARBOXYL)OXIRANE-2-CARBOXYLATE. THIS COMPOUND WAS REMARK 600 DESIGNED FROM THE NATURAL PRODUCT E-64. E-64-C CONSISTS OF REMARK 600 L-TRANSEPOXYSUCCINYL, L-LEUCYL, AND ISOAMYLAMIDE MOIETIES, REMARK 600 AND THE CARBON ATOMS OF THE EPOXY RING HAVE AN R REMARK 600 CONFIGURATION IN THIS COMPLEX. NOTE THAT THE BOND BETWEEN REMARK 600 ATOMS O1 AND C2 IS BROKEN WHEN E-64-C BINDS TO PAPAIN IN REMARK 600 THIS STRUCTURE. REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. STRANDS 4, 5, 6 OF S1A ARE REMARK 700 IDENTICAL TO STRANDS 2, 3, 4 OF SHEET S1B. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E6C A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOH A 214 DBREF 1PPP A 1 212 UNP P00784 PAPA_CARPA 134 345 SEQADV 1PPP GLN A 47 UNP P00784 GLU 180 CONFLICT SEQADV 1PPP GLN A 118 UNP P00784 GLU 251 CONFLICT SEQADV 1PPP GLN A 135 UNP P00784 GLU 268 CONFLICT SEQRES 1 A 212 ILE PRO GLU TYR VAL ASP TRP ARG GLN LYS GLY ALA VAL SEQRES 2 A 212 THR PRO VAL LYS ASN GLN GLY SER CYS GLY SER CYS TRP SEQRES 3 A 212 ALA PHE SER ALA VAL VAL THR ILE GLU GLY ILE ILE LYS SEQRES 4 A 212 ILE ARG THR GLY ASN LEU ASN GLN TYR SER GLU GLN GLU SEQRES 5 A 212 LEU LEU ASP CYS ASP ARG ARG SER TYR GLY CYS ASN GLY SEQRES 6 A 212 GLY TYR PRO TRP SER ALA LEU GLN LEU VAL ALA GLN TYR SEQRES 7 A 212 GLY ILE HIS TYR ARG ASN THR TYR PRO TYR GLU GLY VAL SEQRES 8 A 212 GLN ARG TYR CYS ARG SER ARG GLU LYS GLY PRO TYR ALA SEQRES 9 A 212 ALA LYS THR ASP GLY VAL ARG GLN VAL GLN PRO TYR ASN SEQRES 10 A 212 GLN GLY ALA LEU LEU TYR SER ILE ALA ASN GLN PRO VAL SEQRES 11 A 212 SER VAL VAL LEU GLN ALA ALA GLY LYS ASP PHE GLN LEU SEQRES 12 A 212 TYR ARG GLY GLY ILE PHE VAL GLY PRO CYS GLY ASN LYS SEQRES 13 A 212 VAL ASP HIS ALA VAL ALA ALA VAL GLY TYR GLY PRO ASN SEQRES 14 A 212 TYR ILE LEU ILE LYS ASN SER TRP GLY THR GLY TRP GLY SEQRES 15 A 212 GLU ASN GLY TYR ILE ARG ILE LYS ARG GLY THR GLY ASN SEQRES 16 A 212 SER TYR GLY VAL CYS GLY LEU TYR THR SER SER PHE TYR SEQRES 17 A 212 PRO VAL LYS ASN HET E6C A 213 22 HET MOH A 214 2 HETNAM E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL- HETNAM 2 E6C BUTANE HETNAM MOH METHANOL FORMUL 2 E6C C15 H28 N2 O5 FORMUL 3 MOH C H4 O FORMUL 4 HOH *205(H2 O) HELIX 1 L1 SER A 24 THR A 42 1INCLUDING 3/10 REGION 19 HELIX 2 L2 GLU A 50 ASP A 57 1 8 HELIX 3 L3 TYR A 67 TYR A 78 1 12 HELIX 4 R1 ASN A 117 ASN A 127 1INCLUDING 3/10 REGION 11 HELIX 5 R2 GLY A 138 GLN A 142 1INCLUDING 3/10 REGION 5 SHEET 1 S1A 6 ASP A 108 VAL A 113 0 SHEET 2 S1A 6 SER A 206 VAL A 210 -1 O SER A 206 N VAL A 113 SHEET 3 S1A 6 VAL A 130 LEU A 134 -1 O SER A 131 N PHE A 207 SHEET 4 S1A 6 ASP A 158 GLY A 167 -1 O HIS A 159 N LEU A 134 SHEET 5 S1A 6 TYR A 170 ASN A 175 -1 N LEU A 172 O GLY A 165 SHEET 6 S1A 6 GLY A 185 ARG A 191 -1 N ILE A 189 O ILE A 171 SHEET 1 S1B 4 VAL A 5 TRP A 7 0 SHEET 2 S1B 4 ASP A 158 GLY A 167 -1 N TYR A 166 O VAL A 5 SHEET 3 S1B 4 TYR A 170 ASN A 175 -1 N LEU A 172 O GLY A 165 SHEET 4 S1B 4 GLY A 185 ARG A 191 -1 N ILE A 189 O ILE A 171 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.04 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.05 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.08 LINK SG CYS A 25 C2 E6C A 213 1555 1555 1.80 CISPEP 1 GLY A 151 PRO A 152 0 3.41 SITE 1 AC1 10 GLN A 19 GLY A 23 CYS A 25 TRP A 26 SITE 2 AC1 10 GLY A 65 GLY A 66 VAL A 157 ASP A 158 SITE 3 AC1 10 HIS A 159 HOH A 287 SITE 1 AC2 3 VAL A 5 ASP A 6 TYR A 170 CRYST1 43.370 102.340 49.950 90.00 90.00 90.00 P 21 21 21 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 0.023057 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020020 0.00000