HEADER CYSTEINE PROTEASE 27-MAY-98 1BF7 TITLE MOLECULAR MODEL OF THE CATHEPSIN B-LIKE CYSTEINE PROTEASE TITLE 2 FROM THE PROTOZOAN PARASITE LEISHMANIA MAJOR, THEORETICAL TITLE 3 MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN B-LIKE CYSTEINE PROTEASE; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 STRAIN: LV39 (MRHO/SU/59/P) KEYWDS CYSTEINE PROTEASE, CATHEPSIN B-LIKE, PAPAIN LIKE, OCCLUDING KEYWDS 2 LOOP EXPDTA THEORETICAL MODEL AUTHOR P.M.SELZER,X.CHEN,V.J.CHAN,M.CHENG,G.L.KENYON,I.D.KUNTZ, AUTHOR 2 J.A.SAKANARI,F.E.COHEN,J.H.MCKERROW REVDAT 2 01-APR-03 1BF7 1 JRNL REVDAT 1 12-AUG-98 1BF7 0 JRNL AUTH P.M.SELZER,X.CHEN,V.J.CHAN,M.CHENG,G.L.KENYON, JRNL AUTH 2 I.D.KUNTZ,J.A.SAKANARI,F.E.COHEN,J.H.MCKERROW JRNL TITL LEISHMANIA MAJOR: MOLECULAR MODELING OF CYSTEINE JRNL TITL 2 PROTEASES AND PREDICTION OF NEW NONPEPTIDE JRNL TITL 3 INHIBITORS. JRNL REF EXP.PARASITOL. V. 87 212 1997 JRNL REFN ASTM EXPAAA US ISSN 0014-4894 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES WERE REFINED REMARK 3 USING THE AMBER POTENTIAL FUNCTION WITHIN INSIGHT II. THE REMARK 3 QUALITY OF THE MODEL WAS TESTED WITH QPACK (GREGORET AND REMARK 3 COHEN, 1990, J MOL. BIOL., 211, 959-974), VADAR (UNIVERSITY OF REMARK 3 ALBERTA PROTEIN ENGINEERING NETWORK OF CENTRES OF EXCELLENCE) REMARK 3 AND THE PROFILE METHOD OF LUTHY (LUTHY ET AL., 1992, NATURE REMARK 3 356, 83-85) (PROFILES 3D, INSIGHTII). REMARK 4 REMARK 4 1BF7 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 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 450 REMARK 450 SOURCE REMARK 450 THE ORGANISM IS A PROTOZOAN PARASITE UNDERGOING A LIFE REMARK 450 CYCLE WITHIN DIFFERENT HOSTS (FLY AND VERTEBRATE) THUS REMARK 450 DEVELOPING DIFFERENT STAGES. THE SEQUENCE WHICH WAS USED REMARK 450 TO PRODUCE THE MODEL CAME FROM THE SO-CALLED PROMASTIGOTE REMARK 450 FORM OF THE PARASITE WHICH RESIDES IN THE VECTOR (FLY). 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 VAL A 48 -39.95 93.95 REMARK 500 ASP A 90 -40.38 51.81 REMARK 500 CYS A 91 -39.43 65.41 REMARK 500 LYS A 147 -72.96 128.97 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 45 GLY A 46 -145.15 REMARK 500 GLU A 89 ASP A 90 -143.71 REMARK 500 THR A 118 PRO A 119 -149.00 REMARK 500 GLU A 129 MET A 130 143.61 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CT REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD. REMARK 800 REMARK 800 SITE_IDENTIFIER: S1P REMARK 800 SITE_DESCRIPTION: S1 PRIME SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: S2P REMARK 800 SITE_DESCRIPTION: S2 PRIME SITE, EXOPEPTIDASE ACTIVE REMARK 800 SITE OF THE OCCLUDING LOOP. REMARK 800 REMARK 800 SITE_IDENTIFIER: S1 REMARK 800 SITE_DESCRIPTION: S1 SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: S2 REMARK 800 SITE_DESCRIPTION: S2 SITE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 1BF7 GB 1848229 1 - 97 NOT IN ATOMS LIST REMARK 999 1BF7 GLY 63A - GLY 63A - INSERTED DBREF 1BF7 A 1 242 GB 1848229 AAB48119 98 339 SEQADV 1BF7 GLY A 63A GB 1848229 INSERTION SEQRES 1 A 244 LEU PRO GLU PHE PHE ASP ALA ALA GLU HIS TRP PRO MET SEQRES 2 A 244 CYS LEU THR ILE SER GLU ILE ARG ASP GLN SER ASN CYS SEQRES 3 A 244 GLY SER CYS TRP ALA ILE ALA ALA VAL GLU ALA ILE SER SEQRES 4 A 244 ASP ARG TYR CYS THR PHE GLY GLY VAL PRO ASP ARG ARG SEQRES 5 A 244 MET SER THR SER ASN LEU LEU SER CYS CYS GLY PHE ILE SEQRES 6 A 244 CYS GLY LEU GLY CYS HIS GLY GLY ILE PRO THR VAL ALA SEQRES 7 A 244 TRP LEU TRP TRP VAL TRP VAL GLY ILE ALA THR GLU ASP SEQRES 8 A 244 CYS GLN PRO TYR PRO PHE ASP PRO CYS SER HIS HIS GLY SEQRES 9 A 244 ASN SER GLU LYS TYR PRO PRO CYS PRO SER THR ILE TYR SEQRES 10 A 244 ASP THR PRO LYS CYS ASN THR THR CYS GLU ARG ASN GLU SEQRES 11 A 244 MET ASP LEU VAL LYS TYR LYS GLY SER THR SER TYR SER SEQRES 12 A 244 VAL LYS GLY GLU LYS GLU LEU MET ILE GLU LEU MET THR SEQRES 13 A 244 ASN GLY PRO LEU GLU LEU THR MET GLN VAL TYR SER ASP SEQRES 14 A 244 PHE VAL GLY TYR LYS SER GLY VAL TYR LYS HIS VAL LEU SEQRES 15 A 244 GLY ASP PHE LEU GLY GLY HIS ALA VAL LYS LEU VAL GLY SEQRES 16 A 244 TRP GLY THR GLN ASP GLY VAL PRO TYR TRP LYS VAL ALA SEQRES 17 A 244 ASN SER TRP ASN THR ASP TRP GLY ASP LYS GLY TYR PHE SEQRES 18 A 244 LEU ILE GLN ARG GLY ASN ASN GLU CYS LYS ILE GLU SER SEQRES 19 A 244 GLY GLY VAL ALA GLY ILE PRO ALA GLN GLU HELIX 1 1 ALA A 7 HIS A 10 1 4 HELIX 2 2 CYS A 29 THR A 44 1 16 HELIX 3 3 THR A 55 CYS A 61 1 7 HELIX 4 4 PRO A 74 TRP A 83 1 10 HELIX 5 5 GLU A 148 ASN A 156 1 9 HELIX 6 6 SER A 167 VAL A 170 1 4 HELIX 7 7 GLU A 228 LYS A 230 5 3 SHEET 1 A 4 LEU A 159 GLN A 164 0 SHEET 2 A 4 GLY A 187 GLN A 198 -1 N LEU A 192 O LEU A 159 SHEET 3 A 4 VAL A 201 ALA A 207 -1 N ALA A 207 O LYS A 191 SHEET 4 A 4 TYR A 219 GLN A 223 -1 N ILE A 222 O TRP A 204 SHEET 1 B 2 GLY A 137 SER A 142 0 SHEET 2 B 2 VAL A 236 PRO A 240 -1 N ILE A 239 O SER A 138 SSBOND 1 CYS A 14 CYS A 43 SSBOND 2 CYS A 26 CYS A 69 SSBOND 3 CYS A 61 CYS A 121 SSBOND 4 CYS A 62 CYS A 65 SSBOND 5 CYS A 91 CYS A 125 SSBOND 6 CYS A 99 CYS A 111 SITE 1 CT 3 CYS A 29 HIS A 188 ASN A 208 SITE 1 S1P 2 GLU A 19 TRP A 210 SITE 1 S2P 2 HIS A 101 HIS A 102 SITE 1 S1 4 ILE A 73 PRO A 74 THR A 162 ALA A 189 SITE 1 S2 3 THR A 75 GLY A 234 VAL A 236 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MASTER 84 0 0 7 6 0 5 6 0 0 0 19 END