HEADER HYDROLASE/HYDROLASE INHIBITOR 02-JUL-02 1M43 TITLE CRYSTAL STRUCTURE OF PMII IN COMPLEX WITH PEPSTATIN A TO 2.4 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMEPSIN II; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ASPARTIC HEMOGLOBINASE II, PFAPD; COMPND 5 EC: 3.4.23.39; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPSTATIN; COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_COMMON: MALARIA PARASITE P. FALCIPARUM; SOURCE 4 ORGANISM_TAXID: 5833; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: STREPTOMYCES ARGENTEOLUS SUBSP. TOYONAKENSIS; SOURCE 10 ORGANISM_TAXID: 285516 KEYWDS PLASMEPSIN II, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.A.ASOJO,A.M.SILVA,S.GULNIK REVDAT 5 30-OCT-24 1M43 1 REMARK REVDAT 4 27-OCT-21 1M43 1 SEQADV LINK REVDAT 3 13-JUL-11 1M43 1 VERSN REVDAT 2 24-FEB-09 1M43 1 VERSN REVDAT 1 24-JUL-02 1M43 0 JRNL AUTH O.A.ASOJO,A.M.SILVA,S.GULNIK JRNL TITL NOVEL UNCOMPLEXED AND COMPLEX STRUCTURES OF PM II, AN JRNL TITL 2 ASPARTIC PROTEASE FROM P. FALCIPARUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 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) (%) : 79.5 REMARK 3 NUMBER OF REFLECTIONS : 35694 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) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1761 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4488 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 201 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 555 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.19000 REMARK 3 B12 (A**2) : 1.66000 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) : 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 72.79 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.PARAM 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 1M43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35751 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09660 REMARK 200 R SYM (I) : 0.09660 REMARK 200 FOR THE DATA SET : 17.4300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26000 REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1SME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.85 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 32.63067 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 65.26133 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 65.26133 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 32.63067 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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: 5220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 400 REMARK 400 COMPOUND 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: C, D 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 O GLY B 0 N SER B 1 1.59 REMARK 500 O GLY A 0 N SER A 1 1.68 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 GLY A 0 O - C - N ANGL. DEV. = -41.4 DEGREES REMARK 500 GLY B 0 O - C - N ANGL. DEV. = -47.1 DEGREES REMARK 500 CYS B 285 CA - CB - SG ANGL. DEV. = 6.8 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 A 1 -109.30 41.99 REMARK 500 ASP A 4 -162.20 -69.05 REMARK 500 ASN A 5 84.57 169.88 REMARK 500 ILE A 14 -50.45 -121.48 REMARK 500 GLN A 26 -90.74 64.22 REMARK 500 GLN A 27 91.79 62.04 REMARK 500 LYS A 68 176.16 -59.46 REMARK 500 ASP A 69 -71.39 -166.78 REMARK 500 THR A 71 108.57 -59.45 REMARK 500 LEU A 98 141.21 -179.04 REMARK 500 SER A 135 85.44 17.98 REMARK 500 ASN A 147 36.31 39.71 REMARK 500 ALA A 152 74.52 -69.55 REMARK 500 HIS A 161 -89.47 -4.85 REMARK 500 ASP A 162 38.82 -96.70 REMARK 500 LYS A 163 -53.23 -126.27 REMARK 500 LEU A 191 -85.42 -131.11 REMARK 500 VAL A 201 -83.53 -104.15 REMARK 500 GLN A 232 -97.18 -63.25 REMARK 500 ASP A 235 63.73 -103.81 REMARK 500 PRO A 243 49.91 -80.74 REMARK 500 PRO A 297 107.98 -29.23 REMARK 500 SER B 1 -142.06 -97.65 REMARK 500 GLN B 12 55.06 37.15 REMARK 500 ILE B 14 -30.98 -138.94 REMARK 500 GLN B 26 32.46 78.28 REMARK 500 LEU B 33 90.33 -66.91 REMARK 500 THR B 49 156.03 -35.13 REMARK 500 LYS B 62 -5.46 -162.66 REMARK 500 ASP B 69 -48.91 -146.38 REMARK 500 VAL B 82 145.17 -178.39 REMARK 500 ASN B 95 -6.28 -156.40 REMARK 500 PHE B 102 -157.37 -136.92 REMARK 500 LEU B 126 26.56 -143.79 REMARK 500 SER B 135 81.80 39.04 REMARK 500 ALA B 152 79.70 -69.93 REMARK 500 HIS B 161 -55.02 -10.96 REMARK 500 LYS B 163 -42.96 -136.17 REMARK 500 ASP B 190 53.82 -100.31 REMARK 500 LEU B 191 -93.41 -108.58 REMARK 500 LYS B 208 53.37 38.02 REMARK 500 PHE B 241 13.25 58.62 REMARK 500 PRO B 243 32.76 -78.45 REMARK 500 LYS B 253 -6.60 -56.79 REMARK 500 PRO B 282 -72.54 -35.95 REMARK 500 HIS B 318 60.16 37.01 REMARK 500 ASN B 328 172.14 -42.83 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 C 650 ALA C 651 -124.58 REMARK 500 STA D 4 ALA D 5 -121.07 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 GLY A 0 47.34 REMARK 500 GLY B 0 49.54 REMARK 500 STA C 650 24.94 REMARK 500 STA D 4 27.03 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 C 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: 1SME RELATED DB: PDB REMARK 900 PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM REMARK 900 FALCIPARUM, IN COMPLEX WITH PEPSTATIN A DBREF 1M43 A -1 329 UNP P46925 PLM2_PLAFA 123 453 DBREF 1M43 B -1 329 UNP P46925 PLM2_PLAFA 123 453 DBREF 1M43 C 647 652 PDB 1M43 1M43 647 652 DBREF 1M43 D 1 6 PDB 1M43 1M43 1 6 SEQADV 1M43 SER A 205 UNP P46925 MET 329 ENGINEERED MUTATION SEQADV 1M43 SER B 205 UNP P46925 MET 329 ENGINEERED MUTATION 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 SER 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 B 331 LEU GLY SER SER ASN ASP ASN ILE GLU LEU VAL ASP PHE SEQRES 2 B 331 GLN ASN ILE MET PHE TYR GLY ASP ALA GLU VAL GLY ASP SEQRES 3 B 331 ASN GLN GLN PRO PHE THR PHE ILE LEU ASP THR GLY SER SEQRES 4 B 331 ALA ASN LEU TRP VAL PRO SER VAL LYS CYS THR THR ALA SEQRES 5 B 331 GLY CYS LEU THR LYS HIS LEU TYR ASP SER SER LYS SER SEQRES 6 B 331 ARG THR TYR GLU LYS ASP GLY THR LYS VAL GLU MET ASN SEQRES 7 B 331 TYR VAL SER GLY THR VAL SER GLY PHE PHE SER LYS ASP SEQRES 8 B 331 LEU VAL THR VAL GLY ASN LEU SER LEU PRO TYR LYS PHE SEQRES 9 B 331 ILE GLU VAL ILE ASP THR ASN GLY PHE GLU PRO THR TYR SEQRES 10 B 331 THR ALA SER THR PHE ASP GLY ILE LEU GLY LEU GLY TRP SEQRES 11 B 331 LYS ASP LEU SER ILE GLY SER VAL ASP PRO ILE VAL VAL SEQRES 12 B 331 GLU LEU LYS ASN GLN ASN LYS ILE GLU ASN ALA LEU PHE SEQRES 13 B 331 THR PHE TYR LEU PRO VAL HIS ASP LYS HIS THR GLY PHE SEQRES 14 B 331 LEU THR ILE GLY GLY ILE GLU GLU ARG PHE TYR GLU GLY SEQRES 15 B 331 PRO LEU THR TYR GLU LYS LEU ASN HIS ASP LEU TYR TRP SEQRES 16 B 331 GLN ILE THR LEU ASP ALA HIS VAL GLY ASN ILE SER LEU SEQRES 17 B 331 GLU LYS ALA ASN CYS ILE VAL ASP SER GLY THR SER ALA SEQRES 18 B 331 ILE THR VAL PRO THR ASP PHE LEU ASN LYS MET LEU GLN SEQRES 19 B 331 ASN LEU ASP VAL ILE LYS VAL PRO PHE LEU PRO PHE TYR SEQRES 20 B 331 VAL THR LEU CYS ASN ASN SER LYS LEU PRO THR PHE GLU SEQRES 21 B 331 PHE THR SER GLU ASN GLY LYS TYR THR LEU GLU PRO GLU SEQRES 22 B 331 TYR TYR LEU GLN HIS ILE GLU ASP VAL GLY PRO GLY LEU SEQRES 23 B 331 CYS MET LEU ASN ILE ILE GLY LEU ASP PHE PRO VAL PRO SEQRES 24 B 331 THR PHE ILE LEU GLY ASP PRO PHE MET ARG LYS TYR PHE SEQRES 25 B 331 THR VAL PHE ASP TYR ASP ASN HIS SER VAL GLY ILE ALA SEQRES 26 B 331 LEU ALA LYS LYS ASN LEU SEQRES 1 C 6 IVA VAL VAL STA ALA STA SEQRES 1 D 6 IVA VAL VAL STA ALA STA HET IVA C 647 6 HET STA C 650 11 HET STA C 652 12 HET IVA D 1 6 HET STA D 4 11 HET STA D 6 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 *555(H2 O) HELIX 1 1 THR A 49 LYS A 55 5 7 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 TRP A 128 SER A 132 5 5 HELIX 5 5 PRO A 138 GLN A 146 1 9 HELIX 6 6 GLU A 174 ARG A 176 5 3 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 ALA B 50 LYS B 55 5 6 HELIX 11 11 THR B 108 GLU B 112 5 5 HELIX 12 12 TRP B 128 SER B 132 5 5 HELIX 13 13 PRO B 138 GLN B 146 1 9 HELIX 14 14 GLU B 174 TYR B 178 5 5 HELIX 15 15 PRO B 223 ASN B 233 1 11 HELIX 16 16 GLU B 269 LEU B 274 1 6 HELIX 17 17 GLY B 302 LYS B 308 1 7 SHEET 1 A15 TYR A 178 LYS A 186 0 SHEET 2 A15 SER A 319 ALA A 325 -1 N VAL A 320 O GLU A 185 SHEET 3 A15 TYR A 309 ASP A 314 -1 N PHE A 310 O ALA A 323 SHEET 4 A15 LEU A 153 TYR A 157 -1 O PHE A 154 N PHE A 313 SHEET 5 A15 GLY A 166 ILE A 170 -1 O PHE A 167 N TYR A 157 SHEET 6 A15 ILE A 6 PHE A 11 -1 O ILE A 6 N LEU A 168 SHEET 7 A15 MET A 15 GLU A 21 -1 O MET A 15 N PHE A 11 SHEET 8 A15 PRO A 28 ASP A 34 -1 N PHE A 29 O ALA A 20 SHEET 9 A15 GLY A 122 GLY A 125 1 N GLY A 122 O THR A 30 SHEET 10 A15 LEU A 40 PRO A 43 -1 N TRP A 41 O ILE A 123 SHEET 11 A15 LEU A 96 ASP A 107 1 N ILE A 103 O LEU A 40 SHEET 12 A15 THR A 81 VAL A 93 -1 N SER A 83 O ASP A 107 SHEET 13 A15 LYS A 72 ASN A 76 -1 N VAL A 73 O GLY A 84 SHEET 14 A15 THR A 81 VAL A 93 -1 O VAL A 82 N MET A 75 SHEET 15 A15 MET A 15 GLU A 21 -1 O GLU A 21 N THR A 92 SHEET 1 B 7 LYS A 265 LEU A 268 0 SHEET 2 B 7 PHE A 257 THR A 260 -1 N PHE A 257 O LEU A 268 SHEET 3 B 7 GLN A 194 HIS A 200 -1 N ASP A 198 O THR A 260 SHEET 4 B 7 SER A 205 VAL A 213 -1 O LEU A 206 N ALA A 199 SHEET 5 B 7 THR A 298 LEU A 301 1 O PHE A 299 N ILE A 212 SHEET 6 B 7 ILE A 220 VAL A 222 -1 N THR A 221 O ILE A 300 SHEET 7 B 7 ILE A 289 GLY A 291 1 O ILE A 290 N VAL A 222 SHEET 1 C 4 ILE A 237 LYS A 238 0 SHEET 2 C 4 TYR A 245 LEU A 248 -1 O VAL A 246 N ILE A 237 SHEET 3 C 4 LEU A 284 MET A 286 -1 N CYS A 285 O THR A 247 SHEET 4 C 4 GLN A 275 HIS A 276 -1 N GLN A 275 O MET A 286 SHEET 1 D15 THR B 183 LYS B 186 0 SHEET 2 D15 SER B 319 LEU B 324 -1 N VAL B 320 O GLU B 185 SHEET 3 D15 TYR B 309 ASP B 314 -1 O PHE B 310 N ALA B 323 SHEET 4 D15 LEU B 153 TYR B 157 -1 O PHE B 154 N PHE B 313 SHEET 5 D15 GLY B 166 ILE B 170 -1 O PHE B 167 N TYR B 157 SHEET 6 D15 GLU B 7 PHE B 11 -1 N LEU B 8 O GLY B 166 SHEET 7 D15 MET B 15 ASP B 19 -1 O MET B 15 N PHE B 11 SHEET 8 D15 THR B 30 ASP B 34 -1 N PHE B 31 O GLY B 18 SHEET 9 D15 GLY B 122 GLY B 125 1 N GLY B 122 O THR B 30 SHEET 10 D15 LEU B 40 PRO B 43 -1 N TRP B 41 O ILE B 123 SHEET 11 D15 LEU B 96 ASP B 107 1 O ILE B 103 N VAL B 42 SHEET 12 D15 GLY B 80 VAL B 93 -1 O SER B 83 N ILE B 106 SHEET 13 D15 GLU B 21 VAL B 22 -1 O GLU B 21 N THR B 92 SHEET 14 D15 GLY B 80 VAL B 93 -1 N THR B 92 O GLU B 21 SHEET 15 D15 GLU B 67 TYR B 77 -1 O GLU B 67 N LYS B 88 SHEET 1 E 7 LYS B 265 LEU B 268 0 SHEET 2 E 7 PHE B 257 THR B 260 -1 N PHE B 257 O LEU B 268 SHEET 3 E 7 GLN B 194 HIS B 200 -1 N ASP B 198 O THR B 260 SHEET 4 E 7 SER B 205 VAL B 213 -1 N LEU B 206 O ALA B 199 SHEET 5 E 7 THR B 298 LEU B 301 1 O PHE B 299 N ILE B 212 SHEET 6 E 7 ILE B 220 VAL B 222 -1 N THR B 221 O ILE B 300 SHEET 7 E 7 ILE B 289 GLY B 291 1 O ILE B 290 N VAL B 222 SHEET 1 F 4 ILE B 237 LYS B 238 0 SHEET 2 F 4 TYR B 245 LEU B 248 -1 N VAL B 246 O ILE B 237 SHEET 3 F 4 LEU B 284 MET B 286 -1 O CYS B 285 N THR B 247 SHEET 4 F 4 GLN B 275 HIS B 276 -1 O GLN B 275 N MET B 286 SSBOND 1 CYS A 47 CYS A 52 1555 1555 2.03 SSBOND 2 CYS A 249 CYS A 285 1555 1555 2.03 SSBOND 3 CYS B 47 CYS B 52 1555 1555 2.60 SSBOND 4 CYS B 249 CYS B 285 1555 1555 2.65 LINK C IVA C 647 N VAL C 648 1555 1555 1.33 LINK C VAL C 649 N STA C 650 1555 1555 1.34 LINK C STA C 650 N ALA C 651 1555 1555 1.35 LINK C ALA C 651 N STA C 652 1555 1555 1.34 LINK C IVA D 1 N VAL D 2 1555 1555 1.33 LINK C VAL D 3 N STA D 4 1555 1555 1.32 LINK C STA D 4 N ALA D 5 1555 1555 1.34 LINK C ALA D 5 N STA D 6 1555 1555 1.33 CISPEP 1 GLU A 112 PRO A 113 0 0.34 CISPEP 2 GLU B 112 PRO B 113 0 -0.01 SITE 1 AC1 15 ASP A 34 GLY A 36 ASN A 76 TYR A 77 SITE 2 AC1 15 VAL A 78 SER A 79 LEU A 131 TYR A 192 SITE 3 AC1 15 ASP A 214 GLY A 216 THR A 217 SER A 218 SITE 4 AC1 15 PHE B 241 HOH C 737 HOH C 894 SITE 1 AC2 16 PHE A 241 LEU A 242 ASP B 34 GLY B 36 SITE 2 AC2 16 ASN B 76 TYR B 77 VAL B 78 SER B 79 SITE 3 AC2 16 TYR B 192 ASP B 214 GLY B 216 THR B 217 SITE 4 AC2 16 SER B 218 ILE B 290 HOH D 686 HOH D 867 CRYST1 142.235 142.235 97.892 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 0.007031 0.004059 0.000000 0.00000 SCALE2 0.000000 0.008118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010215 0.00000