1QYJ - Header Asymmetric Unit

HEADER HYDROLASE 11-SEP-03 1QYJ

TITLE HISTOASPARTIC PROTEINASE FROM PLASMODIUM FALCIPARUM

COMPND MOL_ID: 1; COMPND 2 MOLECULE: HAP PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 124-451 OF SWS Q9Y006; COMPND 5 OTHER_DETAILS: HISTOASPARTIC PROTEINASE

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_COMMON: MALARIA PARASITE; SOURCE 4 STRAIN: HB3

KEYWDS PROTEINASE, HYDROLASE, HAEMOGLOBINASE, MALARIA, HOMOLOGY KEYWDS 2 MODELLING

EXPDTA THEORETICAL MODEL

AUTHOR M.E.POPOV,I.V.KASHPAROV,P.M.BOGDANOVITCH,M.A.STENGACH, AUTHOR 2 N.S.ANDREEVA

REVDAT 1 31-AUG-04 1QYJ 0

JRNL AUTH N.S.ANDREEVA,P.M.BOGDANOVITCH,I.V.KASHPAROV, JRNL AUTH 2 M.E.POPOV,M.A.STENGACH JRNL TITL IS HISTOASPARTIC PROTEASE A SERINE PROTEASE WITH A JRNL TITL 2 PEPSIN-LIKE FOLD? JRNL REF PROTEINS: V. 55 705 2004 JRNL REF 2 STRUCT.,FUNCT.,GENET. JRNL REFN ASTM PSFGEY US ISSN 0887-3585

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.BERRY,M.J.HUMPHREYS,P.MATARU,R.GRANGER, REMARK 1 AUTH 2 P.HORROCKS,R.P.MOON,U.CERTA,R.G.RIDLEY,D.BUR,J.KAY REMARK 1 TITL A DISTINCT MEMBER OF THE ASPARTIC PROTEINASE GENE REMARK 1 TITL 2 FAMILY FROM THE HUMAN MALARIA PARASITE PLASMODIUM REMARK 1 TITL 3 FALCIPARUM REMARK 1 REF FEBS LETT. V. 447 149 1999 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.ANDREEVA,L.RUMSH REMARK 1 TITL ANALYSIS OF CRYSTAL STRUCTURES OF ASPARTIC REMARK 1 TITL 2 PROTEINASES: ON TH ROLE OF AMINO ACID RESIDUES REMARK 1 TITL 3 ADJACENT TO THE CATALYTIC SITE OF PEPSIN-LIKE REMARK 1 TITL 4 ENZYMES REMARK 1 REF PROTEIN SCI. V. 10 2439 2001 REMARK 1 REFN ASTM PRCIEI US ISSN 0961-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.C.PEITSCH,N.GUEX REMARK 1 TITL SWISS-MODEL AND THE SWISS-PDBVIEWER: AN REMARK 1 TITL 2 ENVIRONMENT FOR COMPARATIVE MODELLING REMARK 1 REF ELECTROPHORESIS V. 18 2714 1997 REMARK 1 REFN GE ISSN 0173-0835 REMARK 1 REFERENCE 4 REMARK 1 AUTH B.R.BROOKS,R.E.BRUCCOLERI,B.D.OLAFSON,D.J.STATES, REMARK 1 AUTH 2 S.SWAMINATHAN,M.KARPLUS REMARK 1 TITL CHARMM A PROGRAM FOR MACROMOLECULAR ENERGY REMARK 1 TITL 2 MINIMIZATION, AND DYNAMICS CALCULATIONS REMARK 1 REF J.COMPUT.CHEM. V. 4 187 1983 REMARK 1 REFN ASTM JCCHDD US ISSN 0192-8651

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM 29B1, DEEPVIEW 3.7B2 REMARK 3 AUTHORS : B.R.BROOKS, R.E.BRUCCOLERI, B.D.OLAFSON, REMARK 3 D.J.STATES (CHARMM), N. GUEX, A. DIEMAND, T. REMARK 3 SCHWEDE (DEEPVIEW) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1QYJ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PRAGUE ON 09-OCT-2003. REMARK 100 THE RCSB ID CODE IS RCSB020225.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: HOMOLOGY MODELING PROCEDURE WAS FOLLOWED BY MOLECULAR REMARK 220 DYNAMICS SIMULATION AND MINIMIZATION OF THE AVERAGED REMARK 220 COORDINATES. MODELLING METHOD: PROGRAM "DEEPVIEW" (SWISS REMARK 220 -PDB VIEWER) VERSION 3.7B2; AUTHORS: N.GUEX, M.C. REMARK 220 PEITSCH; ENERGY MINIMIZATION AND MOLECULAR DYNAMICS REMARK 220 PROGRAM: CHARMM VERSION 29B2; AUTHORS B.R.BROOKS, REMARK 220 R.E.BRUCCOLERI,B.D.OLAFSON, D.J.STATES, S.SWAMINATHAN, REMARK 220 M.KARPLUS; 1. INITIAL MINIMIZATION: 500 CONJUGATE REMARK 220 GRADIENT CYCLES. 2. 600 PS OF MOLECULAR DYNAMICS REMARK 220 SIMULATION WITH 1 FS TIMESTEP IN WATER BOX WITH PERIODIC REMARK 220 BOUNDARY CONDITIONS. 3. MINIMIZATION OF THE AVERAGED REMARK 220 STRUCTURE FROM LAST 50 PS OF MOLECULAR DYNAMICS REMARK 220 SIMULATION WITH 200 CONJUGATE GRADIENT CYCLES. DATA REMARK 220 ANALYSIS: PROGRAM PROCHECK, VERSION 3.4, AUTHORS REMARK 220 LASKOWSKI, MCARTHUR, MOSS, THORNTON; THIS MODEL IS BASED REMARK 220 UPON PDB COORDINATE FILE 1SME OF PLASMEPSIN II.

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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 4 CG ASP A 4 OD1 -0.192 REMARK 500 ASP A 4 CG ASP A 4 OD2 0.152 REMARK 500 GLU A 174 CD GLU A 174 OE2 0.185 REMARK 500 ASP A 179 CG ASP A 179 OD2 0.152 REMARK 500 HIS A 189 CB HIS A 189 CG -0.116 REMARK 500 ARG A 260 CZ ARG A 260 NH2 -0.209 REMARK 500 GLU A 295 CD GLU A 295 OE2 0.125 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ALA A 12 N - CA - C ANGL. DEV. =-12.1 DEGREES

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LF4 RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMEPSIN II REMARK 900 RELATED ID: 1SME RELATED DB: PDB REMARK 900 PLASMEPSIN II FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH REMARK 900 PEPSTATIN A

DBREF 1QYJ A 1 328 UNP Q9Y006 Q9Y006 124 451

SEQRES 1 A 328 SER GLU PHE ASP ASN VAL GLU LEU LYS ASP LEU ALA ASN SEQRES 2 A 328 VAL LEU SER PHE GLY GLU ALA LYS LEU GLY ASP ASN GLY SEQRES 3 A 328 GLN LYS PHE ASN PHE LEU PHE HIS THR ALA SER SER ASN SEQRES 4 A 328 VAL TRP VAL PRO SER ILE LYS CYS THR SER GLU SER CYS SEQRES 5 A 328 GLU SER LYS ASN HIS TYR ASP SER SER LYS SER LYS THR SEQRES 6 A 328 TYR GLU LYS ASP ASP THR PRO VAL LYS LEU THR SER LYS SEQRES 7 A 328 ALA GLY THR ILE SER GLY ILE PHE SER LYS ASP LEU VAL SEQRES 8 A 328 THR ILE GLY LYS LEU SER VAL PRO TYR LYS PHE ILE GLU SEQRES 9 A 328 MET THR GLU ILE VAL GLY PHE GLU PRO PHE TYR SER GLU SEQRES 10 A 328 SER ASP VAL ASP GLY VAL PHE GLY LEU GLY TRP LYS ASP SEQRES 11 A 328 LEU SER ILE GLY SER ILE ASP PRO TYR ILE VAL GLU LEU SEQRES 12 A 328 LYS THR GLN ASN LYS ILE GLU GLN ALA VAL TYR SER ILE SEQRES 13 A 328 TYR LEU PRO PRO GLU ASN LYS ASN LYS GLY TYR LEU THR SEQRES 14 A 328 ILE GLY GLY ILE GLU GLU ARG PHE PHE ASP GLY PRO LEU SEQRES 15 A 328 ASN TYR GLU LYS LEU ASN HIS ASP LEU MET TRP GLN VAL SEQRES 16 A 328 ASP LEU ASP VAL HIS PHE GLY ASN VAL SER SER LYS LYS SEQRES 17 A 328 ALA ASN VAL ILE LEU ASP SER ALA THR SER VAL ILE THR SEQRES 18 A 328 VAL PRO THR GLU PHE PHE ASN GLN PHE VAL GLU SER ALA SEQRES 19 A 328 SER VAL PHE LYS VAL PRO PHE LEU SER LEU TYR VAL THR SEQRES 20 A 328 THR CYS GLY ASN THR LYS LEU PRO THR LEU GLU TYR ARG SEQRES 21 A 328 SER PRO ASN LYS VAL TYR THR LEU GLU PRO LYS GLN TYR SEQRES 22 A 328 LEU GLU PRO LEU GLU ASN ILE PHE SER ALA LEU CYS MET SEQRES 23 A 328 LEU ASN ILE VAL PRO ILE ASP LEU GLU LYS ASN THR PHE SEQRES 24 A 328 VAL LEU GLY ASP PRO PHE MET ARG LYS TYR PHE THR VAL SEQRES 25 A 328 TYR ASP TYR ASP ASN HIS THR VAL GLY PHE ALA LEU ALA SEQRES 26 A 328 LYS ASN LEU

HELIX 1 1 SER A 49 SER A 54 5 6 HELIX 2 2 PRO A 113 SER A 118 1 6 HELIX 3 3 PRO A 138 GLN A 146 1 9 HELIX 4 4 THR A 224 ALA A 234 1 11 HELIX 5 5 GLU A 269 LEU A 274 1 6 HELIX 6 6 GLY A 302 ARG A 307 1 6

SHEET 1 M 6 ASP A 4 LEU A 8 0 SHEET 2 M 6 GLY A 166 GLY A 171 -1 N ILE A 170 O ASP A 4 SHEET 3 M 6 VAL A 153 LEU A 158 -1 N SER A 155 O THR A 169 SHEET 4 M 6 PHE A 310 ASP A 314 -1 N TYR A 313 O TYR A 154 SHEET 5 M 6 HIS A 318 ALA A 323 -1 N GLY A 321 O VAL A 312 SHEET 6 M 6 ASN A 183 LEU A 187 -1 N GLU A 185 O VAL A 320 SHEET 1 AN 4 GLN A 27 PHE A 29 0 SHEET 2 AN 4 ALA A 20 LEU A 22 -1 N PHE A 29 O ALA A 20 SHEET 3 AN 4 VAL A 91 ILE A 93 -1 N LYS A 21 O THR A 92 SHEET 4 AN 4 LEU A 96 VAL A 98 -1 N ILE A 93 O LEU A 96 SHEET 1 BN 8 LEU A 8 LYS A 9 0 SHEET 2 BN 8 PHE A 17 GLY A 18 -1 N LYS A 9 O PHE A 17 SHEET 3 BN 8 PHE A 31 HIS A 34 -1 N GLY A 18 O PHE A 31 SHEET 4 BN 8 GLY A 122 GLY A 125 1 N LEU A 32 O GLY A 122 SHEET 5 BN 8 ASN A 39 VAL A 42 -1 N VAL A 123 O TRP A 41 SHEET 6 BN 8 LYS A 101 MET A 105 1 N VAL A 42 O ILE A 103 SHEET 7 BN 8 PHE A 86 LYS A 88 -1 N PHE A 102 O SER A 87 SHEET 8 BN 8 TYR A 66 ASP A 69 -1 N LYS A 88 O GLU A 67 SHEET 1 DN 2 PRO A 72 SER A 77 0 SHEET 2 DN 2 GLY A 80 GLY A 84 -1 N LEU A 75 O ILE A 82 SHEET 1 AC 4 VAL A 204 SER A 206 0 SHEET 2 AC 4 ASP A 198 PHE A 201 -1 N SER A 206 O VAL A 199 SHEET 3 AC 4 LEU A 257 SER A 261 -1 N HIS A 200 O GLU A 258 SHEET 4 AC 4 LYS A 264 LEU A 268 -1 N TYR A 259 O TYR A 266 SHEET 1 BC 5 TRP A 193 LEU A 197 0 SHEET 2 BC 5 ALA A 209 LEU A 213 -1 N VAL A 195 O VAL A 211 SHEET 3 BC 5 ASN A 297 GLY A 302 1 N ILE A 212 O PHE A 299 SHEET 4 BC 5 VAL A 219 VAL A 222 -1 N VAL A 300 O PRO A 291 SHEET 5 BC 5 ASN A 288 ILE A 292 1 N VAL A 222 O VAL A 290 SHEET 1 DC 2 VAL A 236 VAL A 239 0 SHEET 2 DC 2 SER A 243 THR A 247 -1 N PHE A 237 O VAL A 246 SHEET 1 EC 2 GLU A 275 GLU A 278 0 SHEET 2 EC 2 LEU A 284 MET A 286 -1 N GLU A 275 O MET A 286

SSBOND 1 CYS A 47 CYS A 52 SSBOND 2 CYS A 249 CYS A 285

CISPEP 1 GLU A 112 PRO A 113 0 -4.82

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