HEADER HYDROLASE/HYDROLASE INHIBITOR 18-AUG-04 1W6I TITLE PLASMEPSIN II-PEPSTATIN A COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMEPSIN 2 PRECURSOR; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: ASPARTIC PROTEASE, ASPARTIC HEMOGLOBINASE II, PFAPD; COMPND 5 EC: 3.4.23.39; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPSTATIN; COMPND 9 CHAIN: B, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: STREPTOMYCES ARGENTEOLUS SUBSP. TOYONAKENSIS; SOURCE 9 ORGANISM_TAXID: 285516 KEYWDS MALARIA, DRUG, ASPARTIC PROTEASE, PLASMEPSIN, GLYCOPROTEIN, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.LINDBERG,P.-O.JOHANSSON,A.ROSENQUIST,I.KVARNSTROEM,L.VRANG, AUTHOR 2 B.SAMUELSSON,T.UNGE REVDAT 6 20-NOV-24 1W6I 1 LINK REVDAT 5 17-JAN-18 1W6I 1 REMARK REVDAT 4 08-FEB-17 1W6I 1 SOURCE REVDAT 3 13-JUL-11 1W6I 1 VERSN REVDAT 2 24-FEB-09 1W6I 1 VERSN REVDAT 1 05-JUL-06 1W6I 0 JRNL AUTH J.LINDBERG,P.-O.JOHANSSON,A.ROSENQUIST,I.KVARNSTROEM, JRNL AUTH 2 L.VRANG,B.SAMUELSSON,T.UNGE JRNL TITL STRUCTURAL STUDY OF A NOVEL INHIBITOR WITH BULKY P1 SIDE JRNL TITL 2 CHAIN IN COMPLEX WITH PLASMEPSIN II -IMPLICATIONS FOR DRUG JRNL TITL 3 DESIGN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2339704.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 31493 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 SET) : 0.217 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1590 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4931 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 261 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : -2.08000 REMARK 3 B12 (A**2) : 4.41000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.48 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.090 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 42.91 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PEP.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PEP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1W6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1290020819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.386 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31494 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 32.69800 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 65.39600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.39600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.69800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 98.09400 REMARK 400 REMARK 400 COMPOUND REMARK 400 CATALYTIC ACTIVITY: HYDROLYSIS OF THE BONDS LINKING REMARK 400 CERTAIN HYDROPHOBIC RESIDUES IN HEMOGLOBIN OR GLOBIN. REMARK 400 ALSO CLEAVES SMALL MOLECULES SUBSTRATES SUCH AS REMARK 400 ALA-LEU-GLU-ARG-THR-PHE-|-PHE(NO(2))-SER-PHE-PRO-THR. REMARK 400 REMARK 400 THE PEPSTATIN IS OLIGOPEPTIDE, A MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PEPSTATIN REMARK 400 CHAIN: B, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 LEU A -1 REMARK 465 GLY A 0 REMARK 465 LEU C -1 REMARK 465 GLY C 0 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 VAL B1331 CG1 - CB - CG2 ANGL. DEV. = -11.9 DEGREES REMARK 500 STA B1333 CA - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 VAL D1331 CG1 - CB - CG2 ANGL. DEV. = -13.0 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 ILE A 14 -57.73 -146.94 REMARK 500 GLN A 26 -85.80 -33.71 REMARK 500 GLN A 27 79.60 66.57 REMARK 500 ASP A 69 -66.89 -141.96 REMARK 500 ASN A 95 14.03 -158.47 REMARK 500 SER A 135 71.37 41.83 REMARK 500 PRO A 138 152.53 -42.12 REMARK 500 ASN A 147 27.17 42.14 REMARK 500 HIS A 161 -89.12 -16.10 REMARK 500 ASP A 162 31.00 -92.09 REMARK 500 LYS A 163 -63.41 -120.82 REMARK 500 ASP A 190 54.48 -97.41 REMARK 500 LEU A 191 -79.09 -114.78 REMARK 500 VAL A 201 -76.23 -107.25 REMARK 500 ALA A 219 -165.42 -122.85 REMARK 500 GLN A 232 -74.41 -52.59 REMARK 500 ASP A 235 61.19 -118.33 REMARK 500 PRO A 243 49.72 -82.56 REMARK 500 GLN C 12 29.93 49.65 REMARK 500 SER C 61 20.94 -78.55 REMARK 500 SER C 135 60.49 39.31 REMARK 500 HIS C 161 -75.57 -13.95 REMARK 500 LEU C 191 -85.97 -119.99 REMARK 500 LYS C 208 57.86 38.24 REMARK 500 ALA C 219 -168.89 -127.46 REMARK 500 ASN C 233 41.55 -87.78 REMARK 500 PRO C 243 48.35 -82.73 REMARK 500 REMARK 500 REMARK: NULL 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 STA B 1333 ALA B 1334 -124.19 REMARK 500 STA D 1333 ALA D 1334 -124.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 STA B1333 26.79 REMARK 500 STA D1333 25.85 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 CHAIN B OF PEPSTATIN REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF PEPSTATIN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J8J RELATED DB: PDB REMARK 900 A NEW CLASS OF SMALL NON-PEPTIDYL COMPOUNDS BLOCKSPLASMODIUM REMARK 900 FALCIPARUM DEVELOPMENT IN VITRO BY INHIBITINGPLASMEPSINS REMARK 900 RELATED ID: 1LEE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM INCOMPLEX WITH REMARK 900 INHIBITOR RS367 REMARK 900 RELATED ID: 1LF2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM INCOMPLEX WITH REMARK 900 INHIBITOR RS370 REMARK 900 RELATED ID: 1LF3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM INCOMPLEX WITH REMARK 900 INHIBITOR EH58 REMARK 900 RELATED ID: 1LF4 RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMEPSIN II REMARK 900 RELATED ID: 1M43 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PMII IN COMPLEX WITH PEPSTATIN A TO2.4 A REMARK 900 RELATED ID: 1ME6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASEFROM REMARK 900 PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR REMARK 900 RELATED ID: 1PFZ RELATED DB: PDB REMARK 900 PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM REMARK 900 RELATED ID: 1SME RELATED DB: PDB REMARK 900 PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM REMARK 900 FALCIPARUM, IN COMPLEX WITH PEPSTATIN A REMARK 900 RELATED ID: 1W6H RELATED DB: PDB REMARK 900 NOVEL PLASMEPSIN II-INHIBITOR COMPLEX REMARK 900 RELATED ID: 1XDH RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMEPSIN II IN COMPLEX WITH PEPSTATIN A REMARK 900 RELATED ID: 1XE5 RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMEPSIN II IN COMPLEX OF AN PEPSTATINANALOGUE REMARK 900 RELATED ID: 1XE6 RELATED DB: PDB REMARK 900 STRUCTURE OF PLASMEPSIN II IN COMPLEX OF AN PEPSTATINANALOGUE REMARK 900 RELATED ID: 2BJU RELATED DB: PDB REMARK 900 PLASMEPSIN II COMPLEXED WITH A HIGHLY ACTIVE ACHIRAL INHIBITOR REMARK 900 RELATED ID: 2BL3 RELATED DB: PDB REMARK 900 THEORITICAL INTERACTION MODEL OF PLASMEPSIN II FROM PLASMODIUM REMARK 900 FALCIPARUM WITH A LIGAND FROM AN ECODED STATIN COMBINATORIAL LIBRARY DBREF 1W6I A -1 329 UNP P46925 PLM2_PLAFA 123 453 DBREF 1W6I C -1 329 UNP P46925 PLM2_PLAFA 123 453 DBREF 1W6I B 1330 1335 PDB 1W6I 1W6I 1330 1335 DBREF 1W6I D 1330 1335 PDB 1W6I 1W6I 1330 1335 SEQRES 1 A 331 LEU GLY SER SER ASN ASP ASN ILE GLU LEU VAL ASP PHE SEQRES 2 A 331 GLN ASN ILE MET PHE TYR GLY ASP ALA GLU VAL GLY ASP SEQRES 3 A 331 ASN GLN GLN PRO PHE THR PHE ILE LEU ASP THR GLY SER SEQRES 4 A 331 ALA ASN LEU TRP VAL PRO SER VAL LYS CYS THR THR ALA SEQRES 5 A 331 GLY CYS LEU THR LYS HIS LEU TYR ASP SER SER LYS SER SEQRES 6 A 331 ARG THR TYR GLU LYS ASP GLY THR LYS VAL GLU MET ASN SEQRES 7 A 331 TYR VAL SER GLY THR VAL SER GLY PHE PHE SER LYS ASP SEQRES 8 A 331 LEU VAL THR VAL GLY ASN LEU SER LEU PRO TYR LYS PHE SEQRES 9 A 331 ILE GLU VAL ILE ASP THR ASN GLY PHE GLU PRO THR TYR SEQRES 10 A 331 THR ALA SER THR PHE ASP GLY ILE LEU GLY LEU GLY TRP SEQRES 11 A 331 LYS ASP LEU SER ILE GLY SER VAL ASP PRO ILE VAL VAL SEQRES 12 A 331 GLU LEU LYS ASN GLN ASN LYS ILE GLU ASN ALA LEU PHE SEQRES 13 A 331 THR PHE TYR LEU PRO VAL HIS ASP LYS HIS THR GLY PHE SEQRES 14 A 331 LEU THR ILE GLY GLY ILE GLU GLU ARG PHE TYR GLU GLY SEQRES 15 A 331 PRO LEU THR TYR GLU LYS LEU ASN HIS ASP LEU TYR TRP SEQRES 16 A 331 GLN ILE THR LEU ASP ALA HIS VAL GLY ASN ILE MET LEU SEQRES 17 A 331 GLU LYS ALA ASN CYS ILE VAL ASP SER GLY THR SER ALA SEQRES 18 A 331 ILE THR VAL PRO THR ASP PHE LEU ASN LYS MET LEU GLN SEQRES 19 A 331 ASN LEU ASP VAL ILE LYS VAL PRO PHE LEU PRO PHE TYR SEQRES 20 A 331 VAL THR LEU CYS ASN ASN SER LYS LEU PRO THR PHE GLU SEQRES 21 A 331 PHE THR SER GLU ASN GLY LYS TYR THR LEU GLU PRO GLU SEQRES 22 A 331 TYR TYR LEU GLN HIS ILE GLU ASP VAL GLY PRO GLY LEU SEQRES 23 A 331 CYS MET LEU ASN ILE ILE GLY LEU ASP PHE PRO VAL PRO SEQRES 24 A 331 THR PHE ILE LEU GLY ASP PRO PHE MET ARG LYS TYR PHE SEQRES 25 A 331 THR VAL PHE ASP TYR ASP ASN HIS SER VAL GLY ILE ALA SEQRES 26 A 331 LEU ALA LYS LYS ASN LEU SEQRES 1 C 331 LEU GLY SER SER ASN ASP ASN ILE GLU LEU VAL ASP PHE SEQRES 2 C 331 GLN ASN ILE MET PHE TYR GLY ASP ALA GLU VAL GLY ASP SEQRES 3 C 331 ASN GLN GLN PRO PHE THR PHE ILE LEU ASP THR GLY SER SEQRES 4 C 331 ALA ASN LEU TRP VAL PRO SER VAL LYS CYS THR THR ALA SEQRES 5 C 331 GLY CYS LEU THR LYS HIS LEU TYR ASP SER SER LYS SER SEQRES 6 C 331 ARG THR TYR GLU LYS ASP GLY THR LYS VAL GLU MET ASN SEQRES 7 C 331 TYR VAL SER GLY THR VAL SER GLY PHE PHE SER LYS ASP SEQRES 8 C 331 LEU VAL THR VAL GLY ASN LEU SER LEU PRO TYR LYS PHE SEQRES 9 C 331 ILE GLU VAL ILE ASP THR ASN GLY PHE GLU PRO THR TYR SEQRES 10 C 331 THR ALA SER THR PHE ASP GLY ILE LEU GLY LEU GLY TRP SEQRES 11 C 331 LYS ASP LEU SER ILE GLY SER VAL ASP PRO ILE VAL VAL SEQRES 12 C 331 GLU LEU LYS ASN GLN ASN LYS ILE GLU ASN ALA LEU PHE SEQRES 13 C 331 THR PHE TYR LEU PRO VAL HIS ASP LYS HIS THR GLY PHE SEQRES 14 C 331 LEU THR ILE GLY GLY ILE GLU GLU ARG PHE TYR GLU GLY SEQRES 15 C 331 PRO LEU THR TYR GLU LYS LEU ASN HIS ASP LEU TYR TRP SEQRES 16 C 331 GLN ILE THR LEU ASP ALA HIS VAL GLY ASN ILE MET LEU SEQRES 17 C 331 GLU LYS ALA ASN CYS ILE VAL ASP SER GLY THR SER ALA SEQRES 18 C 331 ILE THR VAL PRO THR ASP PHE LEU ASN LYS MET LEU GLN SEQRES 19 C 331 ASN LEU ASP VAL ILE LYS VAL PRO PHE LEU PRO PHE TYR SEQRES 20 C 331 VAL THR LEU CYS ASN ASN SER LYS LEU PRO THR PHE GLU SEQRES 21 C 331 PHE THR SER GLU ASN GLY LYS TYR THR LEU GLU PRO GLU SEQRES 22 C 331 TYR TYR LEU GLN HIS ILE GLU ASP VAL GLY PRO GLY LEU SEQRES 23 C 331 CYS MET LEU ASN ILE ILE GLY LEU ASP PHE PRO VAL PRO SEQRES 24 C 331 THR PHE ILE LEU GLY ASP PRO PHE MET ARG LYS TYR PHE SEQRES 25 C 331 THR VAL PHE ASP TYR ASP ASN HIS SER VAL GLY ILE ALA SEQRES 26 C 331 LEU ALA LYS LYS ASN LEU SEQRES 1 B 6 IVA VAL VAL STA ALA STA SEQRES 1 D 6 IVA VAL VAL STA ALA STA HET IVA B1330 6 HET STA B1333 11 HET STA B1335 12 HET IVA D1330 6 HET STA D1333 11 HET STA D1335 12 HETNAM IVA ISOVALERIC ACID HETNAM STA STATINE FORMUL 3 IVA 2(C5 H10 O2) FORMUL 3 STA 4(C8 H17 N O3) FORMUL 5 HOH *234(H2 O) HELIX 1 1 THR A 49 LEU A 53 5 5 HELIX 2 2 ASP A 59 SER A 63 5 5 HELIX 3 3 THR A 108 GLU A 112 5 5 HELIX 4 4 PRO A 113 SER A 118 1 6 HELIX 5 5 TRP A 128 SER A 132 5 5 HELIX 6 6 PRO A 138 GLN A 146 1 9 HELIX 7 7 PRO A 223 LEU A 231 1 9 HELIX 8 8 GLU A 269 LEU A 274 1 6 HELIX 9 9 GLY A 302 LYS A 308 1 7 HELIX 10 10 GLY C 51 LYS C 55 5 5 HELIX 11 11 ASP C 59 SER C 63 5 5 HELIX 12 12 THR C 108 GLU C 112 5 5 HELIX 13 13 PRO C 113 SER C 118 1 6 HELIX 14 14 TRP C 128 SER C 132 5 5 HELIX 15 15 PRO C 138 GLN C 146 1 9 HELIX 16 16 GLU C 174 ARG C 176 5 3 HELIX 17 17 PRO C 223 ASN C 233 1 11 HELIX 18 18 GLU C 269 LEU C 274 1 6 HELIX 19 19 GLY C 302 LYS C 308 1 7 SHEET 1 AA 3 GLU A 67 ASN A 76 0 SHEET 2 AA 3 THR A 81 VAL A 93 -1 O VAL A 82 N MET A 75 SHEET 3 AA 3 MET A 15 VAL A 22 -1 O GLU A 21 N THR A 92 SHEET 1 AB 7 GLU A 67 ASN A 76 0 SHEET 2 AB 7 THR A 81 VAL A 93 -1 O VAL A 82 N MET A 75 SHEET 3 AB 7 LEU A 96 ASP A 107 -1 O LEU A 96 N VAL A 93 SHEET 4 AB 7 LEU A 40 PRO A 43 1 O LEU A 40 N ILE A 103 SHEET 5 AB 7 GLY A 122 GLY A 125 -1 O ILE A 123 N TRP A 41 SHEET 6 AB 7 PRO A 28 ASP A 34 1 O ILE A 32 N LEU A 124 SHEET 7 AB 7 MET A 15 VAL A 22 -1 O GLY A 18 N PHE A 31 SHEET 1 AC 7 LYS A 265 LEU A 268 0 SHEET 2 AC 7 PHE A 257 THR A 260 -1 O PHE A 257 N LEU A 268 SHEET 3 AC 7 GLN A 194 HIS A 200 -1 O ASP A 198 N THR A 260 SHEET 4 AC 7 MET A 205 VAL A 213 -1 O LEU A 206 N ALA A 199 SHEET 5 AC 7 THR A 298 LEU A 301 1 O PHE A 299 N ILE A 212 SHEET 6 AC 7 ILE A 220 VAL A 222 -1 O THR A 221 N ILE A 300 SHEET 7 AC 7 ILE A 289 GLY A 291 1 O ILE A 290 N VAL A 222 SHEET 1 AD 4 ILE A 237 LYS A 238 0 SHEET 2 AD 4 TYR A 245 LEU A 248 -1 O VAL A 246 N ILE A 237 SHEET 3 AD 4 LEU A 284 MET A 286 -1 O CYS A 285 N THR A 247 SHEET 4 AD 4 GLN A 275 HIS A 276 -1 O GLN A 275 N MET A 286 SHEET 1 CA 3 GLU C 67 TYR C 77 0 SHEET 2 CA 3 GLY C 80 VAL C 93 -1 O GLY C 80 N TYR C 77 SHEET 3 CA 3 MET C 15 VAL C 22 -1 O GLU C 21 N THR C 92 SHEET 1 CB 7 GLU C 67 TYR C 77 0 SHEET 2 CB 7 GLY C 80 VAL C 93 -1 O GLY C 80 N TYR C 77 SHEET 3 CB 7 LEU C 96 ASP C 107 -1 O LEU C 96 N VAL C 93 SHEET 4 CB 7 LEU C 40 PRO C 43 1 O LEU C 40 N ILE C 103 SHEET 5 CB 7 GLY C 122 GLY C 125 -1 O ILE C 123 N TRP C 41 SHEET 6 CB 7 GLN C 27 ASP C 34 1 O ILE C 32 N LEU C 124 SHEET 7 CB 7 MET C 15 VAL C 22 -1 O GLY C 18 N PHE C 31 SHEET 1 CC 4 ILE C 237 LYS C 238 0 SHEET 2 CC 4 TYR C 245 LEU C 248 -1 O VAL C 246 N ILE C 237 SHEET 3 CC 4 LEU C 284 MET C 286 -1 O CYS C 285 N THR C 247 SHEET 4 CC 4 GLN C 275 HIS C 276 -1 O GLN C 275 N MET C 286 SSBOND 1 CYS A 47 CYS A 52 1555 1555 2.05 SSBOND 2 CYS A 249 CYS A 285 1555 1555 2.05 SSBOND 3 CYS C 47 CYS C 52 1555 1555 2.04 SSBOND 4 CYS C 249 CYS C 285 1555 1555 2.04 LINK C IVA B1330 N VAL B1331 1555 1555 1.35 LINK C VAL B1332 N STA B1333 1555 1555 1.33 LINK C STA B1333 N ALA B1334 1555 1555 1.36 LINK C ALA B1334 N STA B1335 1555 1555 1.35 LINK C IVA D1330 N VAL D1331 1555 1555 1.33 LINK C VAL D1332 N STA D1333 1555 1555 1.32 LINK C STA D1333 N ALA D1334 1555 1555 1.37 LINK C ALA D1334 N STA D1335 1555 1555 1.34 CISPEP 1 GLU A 112 PRO A 113 0 1.37 CISPEP 2 GLU C 112 PRO C 113 0 -2.72 SITE 1 AC1 17 ASP A 34 GLY A 36 ASN A 76 TYR A 77 SITE 2 AC1 17 VAL A 78 SER A 79 LEU A 131 TYR A 192 SITE 3 AC1 17 ASP A 214 GLY A 216 THR A 217 SER A 218 SITE 4 AC1 17 ILE A 290 HOH B2133 PHE C 241 LEU C 242 SITE 5 AC1 17 HOH C2054 SITE 1 AC2 17 PHE A 241 LEU A 242 ASP C 34 GLY C 36 SITE 2 AC2 17 ASN C 76 TYR C 77 VAL C 78 SER C 79 SITE 3 AC2 17 ILE C 123 LEU C 131 TYR C 192 ASP C 214 SITE 4 AC2 17 GLY C 216 THR C 217 SER C 218 ILE C 290 SITE 5 AC2 17 HOH D2101 CRYST1 142.290 142.290 98.094 90.00 90.00 120.00 P 31 2 1 12 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 0.007028 0.004058 0.000000 0.00000 SCALE2 0.000000 0.008115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010194 0.00000