HEADER HYDROLASE/HYDROLASE INHIBITOR 25-MAY-95 1GEC TITLE GLYCYL ENDOPEPTIDASE-COMPLEX WITH BENZYLOXYCARBONYL-LEUCINE-VALINE- TITLE 2 GLYCINE-METHYLENE COVALENTLY BOUND TO CYSTEINE 25 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCYL ENDOPEPTIDASE; COMPND 3 CHAIN: E; COMPND 4 EC: 3.4.22.25; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE COMPND 7 INHIBITOR; COMPND 8 CHAIN: I; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.P.OHARA,A.M.HEMMINGS,D.J.BUTTLE,L.H.PEARL REVDAT 5 30-OCT-24 1GEC 1 SEQADV LINK REVDAT 4 13-JUL-11 1GEC 1 VERSN REVDAT 3 24-FEB-09 1GEC 1 VERSN REVDAT 2 01-APR-03 1GEC 1 JRNL REVDAT 1 07-DEC-95 1GEC 0 JRNL AUTH B.P.O'HARA,A.M.HEMMINGS,D.J.BUTTLE,L.H.PEARL JRNL TITL CRYSTAL STRUCTURE OF GLYCYL ENDOPEPTIDASE FROM CARICA JRNL TITL 2 PAPAYA: A CYSTEINE ENDOPEPTIDASE OF UNUSUAL SUBSTRATE JRNL TITL 3 SPECIFICITY. JRNL REF BIOCHEMISTRY V. 34 13190 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7548082 JRNL DOI 10.1021/BI00040A034 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 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 : 12725 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) : 0.196 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 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 : 1672 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 117 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) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.200 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 1GEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173542. 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) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.47667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.95333 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 APPLY THE FOLLOWING TO CHAINS: E, I 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 REMARK 400 THE BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE IS PEPTIDE- REMARK 400 LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 C GLY I 4 C1 0HQ I 5 1.47 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 CYS E 22 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 PRO E 103 C - N - CA ANGL. DEV. = 10.3 DEGREES REMARK 500 PRO E 103 C - N - CD ANGL. DEV. = -15.8 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 E 4 146.54 -171.55 REMARK 500 ASP E 6 99.24 -160.03 REMARK 500 ARG E 65 165.27 86.60 REMARK 500 GLN E 93 -168.60 -112.23 REMARK 500 PRO E 103 124.22 25.47 REMARK 500 LYS E 104 -60.96 -124.31 REMARK 500 GLN E 128 170.03 174.24 REMARK 500 SER E 152 63.29 112.62 REMARK 500 ASP E 158 19.59 -158.76 REMARK 500 ALA E 196 -93.47 78.84 REMARK 500 SER E 197 36.08 76.90 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 TYR E 21 0.07 SIDE CHAIN REMARK 500 TYR E 174 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF BENZYLOXYCARBONYL REMARK 800 -LEUCINE-VALINE-GLYCINE-METHYLENE DBREF 1GEC E 1 216 UNP P05994 PAP4_CARPA 133 348 DBREF 1GEC I 1 5 PDB 1GEC 1GEC 1 5 SEQADV 1GEC LEU E 58 UNP P05994 LYS 190 CONFLICT SEQRES 1 E 216 LEU PRO GLU SER VAL ASP TRP ARG ALA LYS GLY ALA VAL SEQRES 2 E 216 THR PRO VAL LYS HIS GLN GLY TYR CYS GLU SER CYS TRP SEQRES 3 E 216 ALA PHE SER THR VAL ALA THR VAL GLU GLY ILE ASN LYS SEQRES 4 E 216 ILE LYS THR GLY ASN LEU VAL GLU LEU SER GLU GLN GLU SEQRES 5 E 216 LEU VAL ASP CYS ASP LEU GLN SER TYR GLY CYS ASN ARG SEQRES 6 E 216 GLY TYR GLN SER THR SER LEU GLN TYR VAL ALA GLN ASN SEQRES 7 E 216 GLY ILE HIS LEU ARG ALA LYS TYR PRO TYR ILE ALA LYS SEQRES 8 E 216 GLN GLN THR CYS ARG ALA ASN GLN VAL GLY GLY PRO LYS SEQRES 9 E 216 VAL LYS THR ASN GLY VAL GLY ARG VAL GLN SER ASN ASN SEQRES 10 E 216 GLU GLY SER LEU LEU ASN ALA ILE ALA HIS GLN PRO VAL SEQRES 11 E 216 SER VAL VAL VAL GLU SER ALA GLY ARG ASP PHE GLN ASN SEQRES 12 E 216 TYR LYS GLY GLY ILE PHE GLU GLY SER CYS GLY THR LYS SEQRES 13 E 216 VAL ASP HIS ALA VAL THR ALA VAL GLY TYR GLY LYS SER SEQRES 14 E 216 GLY GLY LYS GLY TYR ILE LEU ILE LYS ASN SER TRP GLY SEQRES 15 E 216 PRO GLY TRP GLY GLU ASN GLY TYR ILE ARG ILE ARG ARG SEQRES 16 E 216 ALA SER GLY ASN SER PRO GLY VAL CYS GLY VAL TYR ARG SEQRES 17 E 216 SER SER TYR TYR PRO ILE LYS ASN SEQRES 1 I 5 PHQ LEU VAL GLY 0HQ HET PHQ I 1 10 HET 0HQ I 5 1 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM 0HQ DIAZOMETHANE HETSYN 0HQ DIAZOMETHYL GROUP FORMUL 2 PHQ C8 H7 CL O2 FORMUL 2 0HQ C H2 N2 FORMUL 3 HOH *117(H2 O) HELIX 1 1 CYS E 25 THR E 42 1 18 HELIX 2 2 GLU E 50 CYS E 56 1 7 HELIX 3 3 GLN E 68 ASN E 78 1 11 HELIX 4 4 ALA E 97 VAL E 100 1 4 HELIX 5 5 GLU E 118 HIS E 127 1 10 HELIX 6 6 ARG E 139 GLN E 142 1 4 HELIX 7 7 VAL E 203 GLY E 205 5 3 SHEET 1 A 2 GLY E 109 ARG E 112 0 SHEET 2 A 2 TYR E 211 ILE E 214 -1 N ILE E 214 O GLY E 109 SHEET 1 B 4 VAL E 130 VAL E 134 0 SHEET 2 B 4 HIS E 159 SER E 169 -1 N ALA E 163 O VAL E 130 SHEET 3 B 4 LYS E 172 LYS E 178 -1 N LYS E 178 O THR E 162 SHEET 4 B 4 TYR E 190 ARG E 194 -1 N ILE E 193 O ILE E 175 SSBOND 1 CYS E 22 CYS E 63 1555 1555 2.03 SSBOND 2 CYS E 56 CYS E 95 1555 1555 2.04 SSBOND 3 CYS E 153 CYS E 204 1555 1555 2.03 LINK SG CYS E 25 C1 0HQ I 5 1555 1555 1.85 LINK C1 PHQ I 1 N LEU I 2 1555 1555 1.32 SITE 1 AC1 13 HIS E 18 GLY E 20 GLU E 23 CYS E 25 SITE 2 AC1 13 TRP E 26 ARG E 65 GLY E 66 TYR E 67 SITE 3 AC1 13 VAL E 157 ASP E 158 HOH E 229 HOH E 257 SITE 4 AC1 13 HOH I 30 CRYST1 55.780 55.780 64.430 90.00 90.00 120.00 P 31 3 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 0.017928 0.010350 0.000000 0.00000 SCALE2 0.000000 0.020701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015521 0.00000