PDB Short entry for 1F3Q HEADER HYDROLASE/HYDROLASE INHIBITOR 06-JUN-00 1F3Q TITLE MODEL STRUCTURE OF ACTINIDIN IN COMPLEX WITH ZPACK (N- TITLE 2 BENZYLOXYCARBONYL-L-PHENYL ALANYL-L-ALANINE CHLOROMETHYL TITLE 3 KETONE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTINIDIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.14; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ZPACK (BZO-F-ALM); COMPND 7 CHAIN: I; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACTINIDIA CHINENSIS; SOURCE 3 ORGANISM_COMMON: KIWIFRUIT; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES KEYWDS CYSTEINE PROTEINASE INHIBITOR, THIOL PROTEASE INHIBITOR, KEYWDS 2 HYDROLASE EXPDTA THEORETICAL MODEL AUTHOR S.BHATTACHARYA,A.BANERJEE REVDAT 2 27-DEC-00 1F3Q 1 COMPND SOURCE REVDAT 1 06-DEC-00 1F3Q 0 JRNL AUTH S.BHATTACHARYA,A.PAL,A.BERA,S.CHAKRABORTY,S.GHOSH, JRNL AUTH 2 S.GHOSH,A.BANERJEE JRNL TITL THEORETICAL MODEL STRUCTURE OF ACTINIDIN WITH JRNL TITL 2 DIFFERENT BIOLOGICALLY IMPORTANT INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.I.VARUGHESE,Y.SU,D.CROMWELL,S.HASNAIN,N.-H.XUONG REMARK 1 TITL CRYSTAL STRUCTURE OF ACTINIDIN-E-64 COMPLEX REMARK 1 REF BIOCHEMISTRY V. 31 5172 1992 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.DRENTH,K.H.KALK,H.M.SWEN REMARK 1 TITL BINDING OF CHLOROMETHYL KETONE SUBSTRATE ANALOGUES REMARK 1 TITL 2 TO CRYSTALLINE PAPAIN REMARK 1 REF BIOCHEMISTRY V. 15 3731 1976 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH I.DEY REMARK 1 TITL EXPLORING THE INTERACTION OF SOME REMARK 1 TITL 2 N-BENZYLOXYCARBONYL-L-PHENYL ALANYL-L-ALANINE REMARK 1 TITL 3 KETONES AND BOVINE SPLEEN CATHEPSIN B BY MOLECULAR REMARK 1 TITL 4 MODELING AND BINDING FREE ENERGY CALCULATION REMARK 1 REF J.BIOMOL.STRUCT.DYN. V. 16 891 1999 REMARK 1 REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REFERENCE 4 REMARK 1 AUTH E.N.BAKER REMARK 1 TITL STRUCTURE OF ACTINIDIN, AFTER REFINEMENT AT 1.7 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 141 441 1980 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER INSIGHTII(95.0) REMARK 3 AUTHORS : BIOSYM TECHNOLOGY, SAN DIEGO, CA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F3Q COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 AS A PART OF A MAJOR PROGRAMME OF RESEARCH FOR REMARK 5 UNDERSTANDING SUBSTRATE SPECIFICITY OF THIOL PROTEASES, REMARK 5 WE HAVE TAKEN THE X-RAY CRYSTALLOGRAPHICALLY SOLVED REMARK 5 STRUCTURE OF ACTINIDIN (PDB CODE:1AEC, SOLVED AT 1.86 REMARK 5 RESOLUTION), A THIOL PROTEASE AND THE SUBSTRATE LIKE REMARK 5 INHIBITOR ZPACK (FROM ZPACK-PAPAIN COMPLEX, PDB CODE:6PAD) REMARK 5 AND DOCKED THE INHIBITOR TO THE SUBSTRATE BINDING SITE OF REMARK 5 ACTINIDIN TO VISUALISE THE CONSERVED SIGNATURES OF REMARK 5 BIOLOGICALLY IMPORTANT CONFORMATIONS AND MOTIFS. REMARK 5 IT HAS BEEN REPORTED THAT MOLECULAR SURFACE OF BOTH REMARK 5 THE RECEPTOR AND INHIBITOR AT ACTIVE SITE USUALLY FIT REMARK 5 TOGETHER IN A COMPLEMENTARY FASHION AND THE INTERFACE REMARK 5 OF THE PROTEASE SYSTEM IS NOT CONTINUUM, BUT A SET REMARK 5 DISTINCT SUBSITES WITH DIFFERENT TOPOGRAPHIES AND POLAR REMARK 5 ENVIRONMENTS FOR STUDYING STRUCTURE-FUNCTION RELATIONSHIPS REMARK 5 ON THE STRUCTURAL BASIS. REMARK 6 REMARK 6 DIFFERENCE ACCESSIBLE SURFACE AREA (DASA) STUDY OF ACTINIDIN REMARK 6 WITH AND WITHOUT THE INHIBITOR (ZPACK) SHOW THAT THE REMARK 6 RESIDUES AT THE ACTIVE SITE OF ACTINIDIN: REMARK 6 GLU19, ARG63, ASN66, GLY23, CYS25, TRP26, GLY68, TYR69, REMARK 6 ALA136, ILE160, ASP161, HIS162, ALA163, ALA136, ILE70, REMARK 6 MET211 INTERACT WITH THE INHIBITOR. REMARK 6 REMARK 6 DASA STUDY SUGGESTS HOW BINDING AFFINITY AND MOLECULAR REMARK 6 RECOGNITION AFFECT STRUCTURE-FUNCTION ACTIVITY OF REMARK 6 THE SYSTEM. REMARK 6 REMARK 6 MOLECULAR CONFORMATIONS OF THE INHIBITOR (ZPACK) FALL IN THE REMARK 6 ALLOWED REGION OF STEREOCHEMISTRY AND ALL THE CONFORMATIONS REMARK 6 ACTINIDIN EITHER FALL IN THE ALLOWED REGION OR IN REMARK 6 THE EXTENDED ALLOWED REGION OF THE RAMACHANDRAN PLOT REMARK 6 SIGNIFYING THAT THE IS OF THE CORRECT AND SIMILAR REMARK 6 CONFORMATION TO THAT OF REPORTED OTHER THIOL REMARK 6 PROTEASE-INHIBITOR COMPLEX. REMARK 7 REMARK 7 MODEL BUILDING OF THE INHIBITOR(ZPACK) IN COMPLEX WITH REMARK 7 ACTINIDIN WAS PERFORMED ON A SILICON GRAPHICS INDIGO REMARK 7 WORKSTATION USING THE COMMERCIAL SOFTWARE PACKAGE REMARK 7 INSIGHT-II (BIOSYM TECHNOLOGY, SAN DIEGO, CA). REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-2000. REMARK 100 THE RCSB ID CODE IS RCSB011205. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 GLU A 87 CG CD OE1 OE2 REMARK 470 TYR A 218 O 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 M RES CSSEQI PSI PHI REMARK 500 GLN A 60 -106.39 43.75 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C7X RELATED DB: PDB REMARK 900 1C7X CONTAINS MODEL STRUCTURE OF A CARICAIN D158E MUTANT IN REMARK 900 COMPLEX WITH ZPACK REMARK 900 RELATED ID: 1EUX RELATED DB: PDB REMARK 900 1EUX CONTAINS MODEL STRUCTURE OF A CARICAIN D158E MUTANT IN REMARK 900 COMPLEX WITH E-64C REMARK 900 RELATED ID: 1F1I RELATED DB: PDB REMARK 900 1F1I CONTAINS MODEL STRUCTURE OF A CARICAIN D158E MUTANT IN REMARK 900 COMPLEX WITH LEUPEPTIN (ACETYL-L-LEUCYL-L-LEUCYL-L-ARGINAL) DBREF 1F3Q A 1 218 UNP P00785 ACTN_ACTCH 127 344 SEQADV 1F3Q VAL A 100 UNP P00785 LEU 226 CONFLICT SEQADV 1F3Q ALA A 101 UNP P00785 ASP 227 CONFLICT SEQADV 1F3Q GLN A 146 UNP P00785 HIS 272 CONFLICT SEQRES 1 A 218 LEU PRO SER TYR VAL ASP TRP ARG SER ALA GLY ALA VAL SEQRES 2 A 218 VAL ASP ILE LYS SER GLN GLY GLU CYS GLY GLY CYS TRP SEQRES 3 A 218 ALA PHE SER ALA ILE ALA THR VAL GLU GLY ILE ASN LYS SEQRES 4 A 218 ILE VAL THR GLY VAL LEU ILE SER LEU SER GLU GLN GLU SEQRES 5 A 218 LEU ILE ASP CYS GLY ARG THR GLN ASN THR ARG GLY CYS SEQRES 6 A 218 ASN GLY GLY TYR ILE THR ASP GLY PHE GLN PHE ILE ILE SEQRES 7 A 218 ASN ASN GLY GLY ILE ASN THR GLU GLU ASN TYR PRO TYR SEQRES 8 A 218 THR ALA GLN ASP GLY GLU CYS ASN VAL ALA LEU GLN ASN SEQRES 9 A 218 GLU LYS TYR VAL THR ILE ASP THR TYR GLU ASN VAL PRO SEQRES 10 A 218 TYR ASN ASN GLU TRP ALA LEU GLN THR ALA VAL THR TYR SEQRES 11 A 218 GLN PRO VAL SER VAL ALA LEU ASP ALA ALA GLY ASP ALA SEQRES 12 A 218 PHE LYS GLN TYR SER SER GLY ILE PHE THR GLY PRO CYS SEQRES 13 A 218 GLY THR ALA ILE ASP HIS ALA VAL THR ILE VAL GLY TYR SEQRES 14 A 218 GLY THR GLU GLY GLY ILE ASP TYR TRP ILE VAL LYS ASN SEQRES 15 A 218 SER TRP ASP THR THR TRP GLY GLU GLU GLY TYR MET ARG SEQRES 16 A 218 ILE LEU ARG ASN VAL GLY GLY ALA GLY THR CYS GLY ILE SEQRES 17 A 218 ALA THR MET PRO SER TYR PRO VAL LYS TYR SEQRES 1 I 3 PHQ PHE ALM MODRES 1F3Q PHQ I 1H CARBOBENZOXY GROUP MODRES 1F3Q ALM I 3H ALA 1-METHYL-ALANINAL HET PHQ I 1H 10 HET ALM I 3H 6 HETNAM PHQ FORMIC ACID BENZYL ESTER HETNAM ALM 1-METHYL-ALANINAL HETSYN ALM 3-AMINO-BUTAN-2-ONE FORMUL 2 PHQ C8 H8 O2 FORMUL 2 ALM C4 H9 N O HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 GLY A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 GLY A 57 1 9 HELIX 4 4 ARG A 63 CYS A 65 5 3 HELIX 5 5 TYR A 69 GLY A 81 1 13 HELIX 6 6 ASN A 99 GLU A 105 1 7 HELIX 7 7 ASN A 120 GLN A 131 1 12 HELIX 8 8 GLY A 141 TYR A 147 1 7 HELIX 9 9 GLY A 204 ILE A 208 5 5 SHEET 1 A 5 ILE A 151 PHE A 152 0 SHEET 2 A 5 TYR A 193 LEU A 197 1 O ARG A 195 N PHE A 152 SHEET 3 A 5 ILE A 175 LYS A 181 -1 N TRP A 178 O ILE A 196 SHEET 4 A 5 HIS A 162 GLU A 172 -1 O THR A 165 N LYS A 181 SHEET 5 A 5 VAL A 5 ASP A 6 -1 N VAL A 5 O TYR A 169 SHEET 1 B 5 ILE A 151 PHE A 152 0 SHEET 2 B 5 TYR A 193 LEU A 197 1 O ARG A 195 N PHE A 152 SHEET 3 B 5 ILE A 175 LYS A 181 -1 N TRP A 178 O ILE A 196 SHEET 4 B 5 HIS A 162 GLU A 172 -1 O THR A 165 N LYS A 181 SHEET 5 B 5 VAL A 133 LEU A 137 -1 O VAL A 133 N ILE A 166 SHEET 1 C 2 THR A 112 ASN A 115 0 SHEET 2 C 2 SER A 213 VAL A 216 -1 O TYR A 214 N GLU A 114 SSBOND 1 CYS A 22 CYS A 65 SSBOND 2 CYS A 56 CYS A 98 SSBOND 3 CYS A 156 CYS A 206 LINK CM ALM I 3H SG CYS A 25 LINK SG CYS A 22 SG CYS A 65 LINK SG CYS A 56 SG CYS A 98 LINK SG CYS A 156 SG CYS A 206 CISPEP 1 GLY A 154 PRO A 155 0 3.62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 0.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.000000 0.00000