10 20 30 40 50 60 70 80 2PAD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE (SULFHYDRYL PROTEINASE) 01-NOV-76 2PAD
TITLE BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES TO CRYSTALLINE TITLE 2 PAPAIN
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 J.DRENTH,K.H.KALK,H.M.SWEN
REVDAT 10 13-JUL-11 2PAD 1 VERSN REVDAT 9 24-FEB-09 2PAD 1 VERSN REVDAT 8 17-FEB-84 2PAD 1 REMARK REVDAT 7 30-SEP-83 2PAD 1 REVDAT REVDAT 6 14-SEP-81 2PAD 1 REMARK REVDAT 5 31-DEC-80 2PAD 1 REMARK REVDAT 4 30-DEC-77 2PAD 1 REMARK REVDAT 3 01-NOV-77 2PAD 1 COMPND SOURCE AUTHOR REMARK REVDAT 3 2 1 FORMUL SSBOND REVDAT 2 27-SEP-77 2PAD 1 SEQRES REVDAT 1 12-APR-77 2PAD 0
SPRSDE 12-APR-77 2PAD 3PAP
JRNL AUTH J.DRENTH,K.H.KALK,H.M.SWEN JRNL TITL BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES TO JRNL TITL 2 CRYSTALLINE PAPAIN. JRNL REF BIOCHEMISTRY V. 15 3731 1976 JRNL REFN ISSN 0006-2960 JRNL PMID 952885 JRNL DOI 10.1021/BI00662A014
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.DRENTH,J.N.JANSONIUS,R.KOEKOEK,B.G.WOLTHERS REMARK 1 TITL THE STRUCTURE OF PAPAIN REMARK 1 REF ADV.PROTEIN CHEM. V. 25 79 1971 REMARK 1 REFN ISSN 0065-3233 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.DRENTH,J.N.JANSONIUS,R.KOEKOEK,L.A.A.SLUYTERMAN, REMARK 1 AUTH 2 B.G.WOLTHERS REMARK 1 TITL THE STRUCTURE OF THE PAPAIN MOLECULE REMARK 1 REF PHILOS.TRANS.R.SOC.LONDON, V. 257 231 1970 REMARK 1 REF 2 SER.B REMARK 1 REFN ISSN 0080-4622 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.DRENTH,J.N.JANSONIUS,R.KOEKOEK,H.M.SWEN,B.G.WOLTHERS REMARK 1 TITL STRUCTURE OF PAPAIN REMARK 1 REF NATURE V. 218 929 1968 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 EDIT R.J.FELDMANN REMARK 1 REF ATLAS OF MACROMOLECULAR 255 1976 REMARK 1 REF 2 STRUCTURE ON MICROFICHE REMARK 1 PUBL TRACOR JITCO INC.,ROCKVILLE,MD. REMARK 1 REFN REMARK 1 REFERENCE 5 REMARK 1 EDIT M.O.DAYHOFF REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 121 1972 REMARK 1 REF 2 AND STRUCTURE (DATA SECTION) REMARK 1 PUBL NATIONAL BIOMEDICAL RESEARCH FOUNDATION, SILVER SPRING,MD. REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 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 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 30 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2PAD 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 (%): 51.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 285 REMARK 285 THE ENTRY COORDINATES REMARK 285 ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.
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 22.50023 REMARK 290 SMTRY2 2 0.000000 -0.999085 0.042193 -0.53599 REMARK 290 SMTRY3 2 0.000000 0.043374 0.999085 -25.39487 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 0.999085 -0.042193 -51.24843 REMARK 290 SMTRY3 3 0.000000 -0.043374 -0.999085 -24.29456 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.50023 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 -50.71244 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 1.10032 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 400 REMARK 400 COMPOUND REMARK 400 IN THIS STRUCTURE THE ENZYME IS IRREVERSIBLY INHIBITED BY A REMARK 400 CYSTEINE MOLECULE DISULFIDE BOUND TO THE ACTIVE-SITE- REMARK 400 SULFHYDRYL (CYS-25).
REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET SUBSTRUCTURE OF THIS MOLECULE IS DOUBLY REMARK 700 BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE REMARK 700 SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 4,5,6 REMARK 700 OF S1A ARE IDENTICAL TO STRANDS 2,3,4 OF S1B.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYS A 213
DBREF 2PAD A 1 212 UNP P00784 PAPA1_CARPA 134 345
SEQADV 2PAD GLN A 47 UNP P00784 GLU 180 CONFLICT SEQADV 2PAD GLN A 118 UNP P00784 GLU 251 CONFLICT SEQADV 2PAD 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 CYS A 213 7
HETNAM CYS CYSTEINE
FORMUL 2 CYS C3 H7 N O2 S FORMUL 3 HOH *30(H2 O)
HELIX 1 H1 SER A 24 GLY A 43 1 20 HELIX 2 H2 GLU A 50 ARG A 58 1 9 HELIX 3 H3 TYR A 67 TYR A 78 1 12 HELIX 4 H4 ASN A 117 GLN A 128 1 12 HELIX 5 H5 ALA A 137 LEU A 143 1 7
SHEET 1 S1A 7 ARG A 111 GLN A 112 0 SHEET 2 S1A 7 SER A 206 TYR A 208 -1 N TYR A 208 O ARG A 111 SHEET 3 S1A 7 VAL A 130 SER A 131 -1 N SER A 131 O PHE A 207 SHEET 4 S1A 7 ALA A 162 GLY A 167 -1 N ALA A 163 O VAL A 130 SHEET 5 S1A 7 ASN A 169 ASN A 175 -1 N LYS A 174 O ALA A 162 SHEET 6 S1A 7 GLY A 185 ARG A 191 -1 N ILE A 187 O ILE A 173 SHEET 7 S1A 7 GLU A 183 GLU A 183 -1 N GLU A 183 O TYR A 186 SHEET 1 S1B 5 VAL A 5 TRP A 7 0 SHEET 2 S1B 5 ALA A 162 GLY A 167 -1 N TYR A 166 O VAL A 5 SHEET 3 S1B 5 ASN A 169 ASN A 175 -1 N LEU A 172 O GLY A 165 SHEET 4 S1B 5 GLY A 185 ARG A 191 -1 N ILE A 189 O ILE A 171 SHEET 5 S1B 5 PHE A 149 PHE A 149 1 N PHE A 149 O ARG A 188
SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.07 SSBOND 2 CYS A 56 CYS A 95 1555 1555 1.69 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.06
LINK SG CYS A 25 SG CYS A 213 1555 1555 2.06 LINK ND1 HIS A 159 CB CYS A 213 1555 1555 1.91
CISPEP 1 GLY A 151 PRO A 152 0 -12.60
SITE 1 AC1 4 GLN A 19 CYS A 25 ALA A 136 HIS A 159
CRYST1 45.000 104.300 50.800 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 0.022222 0.000000 0.000000 0.25778
SCALE2 0.000000 -0.009855 0.000208 0.96204
SCALE3 0.000000 -0.000427 -0.019680 0.80185