HEADER HYDROLASE/INHIBITOR 24-MAR-06 2CIO TITLE THE HIGH RESOLUTION X-RAY STRUCTURE OF PAPAIN COMPLEXED WITH FRAGMENTS TITLE 2 OF THE TRYPANOSOMA BRUCEI CYSTEINE PROTEASE INHIBITOR ICP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAPAYA PROTEINASE I, PPI, ALLERGEN, CARP1PAPAIN; COMPND 5 EC: 3.4.22.2; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INHIBITOR OF CYSTEINE PEPTIDASE; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: CYSTEINE PROTEASE INHIBITOR, ICP; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: TWO PEPTIDE FRAGMENTS FROM DIGESTION OF ICP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_TAXID: 3649; SOURCE 4 OTHER_DETAILS: PURCHASED FROM SIGMA; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 7 ORGANISM_TAXID: 5691; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBP117 KEYWDS HYDROLASE/INHIBITOR, COMPLEX HYDROLASE-INHIBITOR, ICP, CYSTEINE KEYWDS 2 PROTEASE, INHIBITOR, TRYPANOSOMA BRUCEI, ALLERGEN, PROTEASE, THIOL KEYWDS 3 PROTEASE, ZYMOGEN, HYDROLASE, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.S.ALPHEY,W.N.HUNTER REVDAT 5 13-DEC-23 2CIO 1 LINK REVDAT 4 24-JAN-18 2CIO 1 SOURCE REVDAT 3 24-FEB-09 2CIO 1 VERSN REVDAT 2 14-JUN-06 2CIO 1 JRNL REVDAT 1 18-MAY-06 2CIO 0 JRNL AUTH M.S.ALPHEY,W.N.HUNTER JRNL TITL HIGH-RESOLUTION COMPLEX OF PAPAIN WITH REMNANTS OF A JRNL TITL 2 CYSTEINE PROTEASE INHIBITOR DERIVED FROM TRYPANOSOMA BRUCEI JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 62 504 2006 JRNL REFN ESSN 1744-3091 JRNL PMID 16754967 JRNL DOI 10.1107/S1744309106014849 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30823 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1551 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) : 6.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 95.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 395 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1690 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.73900 REMARK 3 B22 (A**2) : 0.76400 REMARK 3 B33 (A**2) : -0.02500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1870 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2562 ; 1.416 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 5.617 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;34.339 ;23.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 291 ;13.970 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.949 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 261 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1496 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 940 ; 0.234 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1270 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 185 ; 0.205 ; 0.200 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): 67 ; 0.230 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.221 ; 0.200 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): 1158 ; 1.366 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1817 ; 2.065 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 839 ; 2.911 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 729 ; 3.424 ; 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 BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. LYS211-ASN212 IS AT THE C-TERMINUS OF THE PROTEIN REMARK 3 CHAIN WHERE ELECTRON DENSITY WAS POORLY DEFINED REMARK 4 REMARK 4 2CIO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1290028267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9756 REMARK 200 MONOCHROMATOR : SI(III) REMARK 200 OPTICS : TOROIDAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 95.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 9PAP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% ETHANOL, 0.01M NA ACETATE, PH 7.50 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 21.16150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.84850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.05900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.84850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.16150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.05900 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: PQS 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 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 MET B 1 REMARK 465 SER B 2 REMARK 465 HIS B 3 REMARK 465 ASN B 4 REMARK 465 LEU B 5 REMARK 465 PHE B 6 REMARK 465 THR B 7 REMARK 465 GLU B 8 REMARK 465 GLU B 9 REMARK 465 ASP B 10 REMARK 465 ASN B 11 REMARK 465 ASN B 12 REMARK 465 LYS B 13 REMARK 465 THR B 14 REMARK 465 ILE B 15 REMARK 465 ARG B 16 REMARK 465 MET B 17 REMARK 465 VAL B 18 REMARK 465 ILE B 19 REMARK 465 GLY B 20 REMARK 465 GLU B 21 REMARK 465 THR B 22 REMARK 465 PHE B 23 REMARK 465 THR B 24 REMARK 465 ILE B 25 REMARK 465 GLU B 26 REMARK 465 LEU B 27 REMARK 465 GLU B 28 REMARK 465 SER B 29 REMARK 465 ASN B 30 REMARK 465 PRO B 31 REMARK 465 THR B 32 REMARK 465 THR B 33 REMARK 465 GLY B 34 REMARK 465 TYR B 35 REMARK 465 THR B 36 REMARK 465 TRP B 37 REMARK 465 LEU B 38 REMARK 465 ARG B 39 REMARK 465 SER B 40 REMARK 465 GLY B 41 REMARK 465 LEU B 42 REMARK 465 ALA B 43 REMARK 465 GLY B 44 REMARK 465 THR B 45 REMARK 465 GLU B 46 REMARK 465 LEU B 47 REMARK 465 SER B 48 REMARK 465 ASP B 49 REMARK 465 CYS B 50 REMARK 465 THR B 51 REMARK 465 PHE B 52 REMARK 465 ALA B 53 REMARK 465 ILE B 54 REMARK 465 GLN B 55 REMARK 465 SER B 56 REMARK 465 LYS B 57 REMARK 465 PHE B 58 REMARK 465 ASN B 59 REMARK 465 ASN B 60 REMARK 465 ARG B 61 REMARK 465 ALA B 62 REMARK 465 PRO B 63 REMARK 465 HIS B 64 REMARK 465 ASP B 65 REMARK 465 ASN B 66 REMARK 465 HIS B 67 REMARK 465 LYS B 68 REMARK 465 ASN B 69 REMARK 465 HIS B 70 REMARK 465 ARG B 71 REMARK 465 ARG B 72 REMARK 465 LEU B 73 REMARK 465 LEU B 74 REMARK 465 VAL B 75 REMARK 465 GLY B 76 REMARK 465 ALA B 77 REMARK 465 MET B 81 REMARK 465 VAL B 82 REMARK 465 LEU B 83 REMARK 465 GLU B 84 REMARK 465 VAL B 85 REMARK 465 LYS B 86 REMARK 465 ALA B 87 REMARK 465 LEU B 88 REMARK 465 LYS B 89 REMARK 465 ALA B 90 REMARK 465 GLY B 91 REMARK 465 LYS B 92 REMARK 465 HIS B 93 REMARK 465 THR B 94 REMARK 465 TYR B 99 REMARK 465 GLY B 100 REMARK 465 ARG B 101 REMARK 465 PRO B 102 REMARK 465 TRP B 103 REMARK 465 VAL B 104 REMARK 465 GLY B 105 REMARK 465 PHE B 106 REMARK 465 ASN B 107 REMARK 465 ALA B 108 REMARK 465 ALA B 109 REMARK 465 ALA B 110 REMARK 465 LYS B 111 REMARK 465 ARG B 112 REMARK 465 TYR B 113 REMARK 465 ASN B 114 REMARK 465 ILE B 115 REMARK 465 HIS B 116 REMARK 465 VAL B 117 REMARK 465 GLU B 118 REMARK 465 ALA B 119 REMARK 465 THR B 120 REMARK 465 ALA B 121 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 THR B 80 CA C O CB OG1 CG2 REMARK 470 ALA B 98 CA C O CB 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 HOH A 2061 O HOH A 2156 1.98 REMARK 500 CB ALA A 76 O HOH A 2063 2.04 REMARK 500 OE1 GLU A 3 O HOH A 2004 2.10 REMARK 500 O HOH A 2071 O HOH A 2072 2.16 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 2072 O HOH A 2140 4455 1.92 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 TYR A 78 -89.72 -117.98 REMARK 500 ASP A 158 14.38 -157.15 REMARK 500 THR A 193 -166.51 -59.06 REMARK 500 SER A 205 104.11 -160.33 REMARK 500 REMARK 500 REMARK: NULL 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. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1217 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BP4 RELATED DB: PDB REMARK 900 USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF REMARK 900 CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR REMARK 900 COMPLEXES DEMONSTRATE BINDING TO S '-SUBSITES. REMARK 900 RELATED ID: 1BQI RELATED DB: PDB REMARK 900 USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF REMARK 900 CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR REMARK 900 COMPLEXES DEMONSTRATE BINDING TO S '-SUBSITES. REMARK 900 RELATED ID: 1CVZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF PAPAIN WITH CLIK148(CATHEPSIN L REMARK 900 SPECIFIC INHIBITOR) REMARK 900 RELATED ID: 1EFF RELATED DB: PDB REMARK 900 KNOWLEDGE BASED MODEL OF AN INHIBITOR BOUND TO A THIOL(CYSTEIN) REMARK 900 PROTEASE, PAPAIN COMPLEXED WITH NAPQI REMARK 900 RELATED ID: 1KHP RELATED DB: PDB REMARK 900 MONOCLINIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX REMARK 900 RELATED ID: 1KHQ RELATED DB: PDB REMARK 900 ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX REMARK 900 RELATED ID: 1PAD RELATED DB: PDB REMARK 900 PAPAIN -ACETYL-ALANYL-ALANYL- PHENYLALANYL- METHYLENYLALANYL REMARK 900 DERIVATIVE OF CYSTEINE 25 (/ ACAAPACK) REMARK 900 RELATED ID: 1PE6 RELATED DB: PDB REMARK 900 PAPAIN COMPLEX WITH E-64-C REMARK 900 RELATED ID: 1PIP RELATED DB: PDB REMARK 900 PAPAIN COMPLEX WITH SUCCINYL-GLN-VAL-VAL- ALA-ALA-P-NITROANILIDE REMARK 900 RELATED ID: 1POP RELATED DB: PDB REMARK 900 PAPAIN COMPLEX WITH LEUPEPTIN (N-ACETYL-L- LEUCYL-L-LEUCYL-L- REMARK 900 ARGININAL) REMARK 900 RELATED ID: 1PPD RELATED DB: PDB REMARK 900 2-HYDROXYETHYLTHIOPAPAIN - CRYSTAL FORM D REMARK 900 RELATED ID: 1PPN RELATED DB: PDB REMARK 900 PAPAIN CYS-25 WITH BOUND ATOM REMARK 900 RELATED ID: 1PPP RELATED DB: PDB REMARK 900 PAPAIN COMPLEX WITH E64-C (FORM II) REMARK 900 RELATED ID: 1STF RELATED DB: PDB REMARK 900 PAPAIN (CYS 25 CARBOXYMETHYLATED) COMPLEXED WITH THE INHIBITOR REMARK 900 STEFIN B (CYSTATIN B) MUTANT WITH CYS I 8 REPLACED BY SER (C( I 8)S) REMARK 900 RELATED ID: 2PAD RELATED DB: PDB REMARK 900 PAPAIN -CYSTEINYL DERIVATIVE OF CYSTEINE-25 (/PAPSSCYS) REMARK 900 RELATED ID: 4PAD RELATED DB: PDB REMARK 900 PAPAIN -TOSYL-METHYLENYLLYSYL DERIVATIVE OF CYSTEINE-25 (/TLCK) REMARK 900 RELATED ID: 5PAD RELATED DB: PDB REMARK 900 PAPAIN -BENZYLOXYCARBONYL-GLYCYL- PHENYLALANYL- METHYLENYLGLYCYL REMARK 900 DERIVATIVE (/ZGPGCK) REMARK 900 RELATED ID: 6PAD RELATED DB: PDB REMARK 900 PAPAIN -BENZYLOXYCARBONYL- PHENYLALANYL- METHYLENYLALANYL REMARK 900 DERIVATIVE (/ZPACK) REMARK 900 RELATED ID: 9PAP RELATED DB: PDB REMARK 900 PAPAIN CYS-25 OXIDIZED REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN USED IN EXPERIMENT WAS COMMERCIALLY AVAILABLE AND REMARK 999 ALREADY HAD REMOVED SIGNAL AND PROPEPTIDE SEQUENCE FROM N- REMARK 999 TERMINUS. DBREF 2CIO A 1 212 UNP P00784 PAPA1_CARPA 134 345 DBREF 2CIO B 1 121 UNP Q868H0 Q868H0_9TRYP 1 121 SEQADV 2CIO GLN A 47 UNP P00784 GLU 180 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 OCS 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 GLU GLY ALA LEU LEU TYR SER ILE ALA ASN GLN PRO VAL SEQRES 11 A 212 SER VAL VAL LEU GLU 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 SEQRES 1 B 121 MET SER HIS ASN LEU PHE THR GLU GLU ASP ASN ASN LYS SEQRES 2 B 121 THR ILE ARG MET VAL ILE GLY GLU THR PHE THR ILE GLU SEQRES 3 B 121 LEU GLU SER ASN PRO THR THR GLY TYR THR TRP LEU ARG SEQRES 4 B 121 SER GLY LEU ALA GLY THR GLU LEU SER ASP CYS THR PHE SEQRES 5 B 121 ALA ILE GLN SER LYS PHE ASN ASN ARG ALA PRO HIS ASP SEQRES 6 B 121 ASN HIS LYS ASN HIS ARG ARG LEU LEU VAL GLY ALA GLY SEQRES 7 B 121 GLY THR MET VAL LEU GLU VAL LYS ALA LEU LYS ALA GLY SEQRES 8 B 121 LYS HIS THR LEU SER LEU ALA TYR GLY ARG PRO TRP VAL SEQRES 9 B 121 GLY PHE ASN ALA ALA ALA LYS ARG TYR ASN ILE HIS VAL SEQRES 10 B 121 GLU ALA THR ALA MODRES 2CIO OCS A 25 CYS CYSTEINESULFONIC ACID HET OCS A 25 9 HET GOL A1216 6 HET GOL A1217 6 HET ACT A1218 8 HET ACT A1219 4 HET ACT A1220 4 HETNAM OCS CYSTEINESULFONIC ACID HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 OCS C3 H7 N O5 S FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 ACT 3(C2 H3 O2 1-) FORMUL 8 HOH *161(H2 O) HELIX 1 1 TRP A 26 GLY A 43 1 18 HELIX 2 2 SER A 49 ASP A 57 1 9 HELIX 3 3 TYR A 67 TYR A 78 1 12 HELIX 4 4 ASN A 117 GLN A 128 1 12 HELIX 5 5 GLY A 138 LEU A 143 1 6 HELIX 6 6 GLY A 198 LEU A 202 5 5 SHEET 1 AA 3 VAL A 5 ASP A 6 0 SHEET 2 AA 3 HIS A 159 GLY A 167 -1 O TYR A 166 N VAL A 5 SHEET 3 AA 3 VAL A 130 LEU A 134 -1 O VAL A 130 N ALA A 163 SHEET 1 AB 4 VAL A 5 ASP A 6 0 SHEET 2 AB 4 HIS A 159 GLY A 167 -1 O TYR A 166 N VAL A 5 SHEET 3 AB 4 TYR A 170 LYS A 174 -1 O TYR A 170 N GLY A 167 SHEET 4 AB 4 TYR A 186 LYS A 190 -1 O ILE A 187 N ILE A 173 SHEET 1 AC 2 GLY A 109 GLN A 112 0 SHEET 2 AC 2 PHE A 207 VAL A 210 -1 O TYR A 208 N ARG A 111 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.06 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.04 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.07 LINK C SER A 24 N OCS A 25 1555 1555 1.33 LINK C OCS A 25 N TRP A 26 1555 1555 1.33 CISPEP 1 GLY A 151 PRO A 152 0 -1.49 CISPEP 2 LYS A 211 ASN A 212 0 -12.15 SITE 1 AC1 6 LYS A 17 ASN A 18 ARG A 83 ARG A 93 SITE 2 AC1 6 TYR A 94 HOH A2014 SITE 1 AC2 6 GLU A 3 ARG A 59 GLY A 138 LYS A 139 SITE 2 AC2 6 ASP A 140 HOH A2121 SITE 1 AC3 6 CYS A 56 TYR A 78 CYS A 95 ARG A 98 SITE 2 AC3 6 GOL A1217 HOH A2158 SITE 1 AC4 5 VAL A 13 THR A 14 PRO A 15 VAL A 16 SITE 2 AC4 5 TYR A 186 SITE 1 AC5 12 GLU A 3 TYR A 4 ARG A 59 GLN A 73 SITE 2 AC5 12 LEU A 74 GLN A 77 TYR A 78 ACT A1220 SITE 3 AC5 12 HOH A2004 HOH A2047 HOH A2050 HOH A2064 CRYST1 42.323 46.118 95.697 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 0.023628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010450 0.00000