HEADER HYDROLASE/HYDROLASE INHIBITOR 26-DEC-08 3FNT TITLE CRYSTAL STRUCTURE OF PEPSTATIN A BOUND HISTO-ASPARTIC PROTEASE (HAP) TITLE 2 FROM PLASMODIUM FALCIPARUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HAP PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HISTO-ASPARTIC PROTEASE (HAP); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INHIBITOR, (IVA)VV(STA)A(STA); COMPND 8 CHAIN: I; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: HAP, PF14_0078; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI B (DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32B(+); SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: STREPTOMYCES ARGENTEOLUS SUBSP. TOYONAKENSIS; SOURCE 14 ORGANISM_TAXID: 285516; SOURCE 15 OTHER_DETAILS: UNSPECIFIED KEYWDS HISTO-ASPARTIC PROTEASE, HAP, PLASMEPSIN, PEPSTATIN A, ASPARTIC KEYWDS 2 PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.BHAUMIK,A.GUSTCHINA,A.WLODAWER REVDAT 5 22-NOV-23 3FNT 1 REMARK REVDAT 4 06-SEP-23 3FNT 1 REMARK LINK REVDAT 3 01-NOV-17 3FNT 1 REMARK REVDAT 2 13-JUL-11 3FNT 1 VERSN REVDAT 1 12-MAY-09 3FNT 0 JRNL AUTH P.BHAUMIK,H.XIAO,C.L.PARR,Y.KISO,A.GUSTCHINA,R.Y.YADA, JRNL AUTH 2 A.WLODAWER JRNL TITL CRYSTAL STRUCTURES OF THE HISTO-ASPARTIC PROTEASE (HAP) FROM JRNL TITL 2 PLASMODIUM FALCIPARUM. JRNL REF J.MOL.BIOL. V. 388 520 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19285084 JRNL DOI 10.1016/J.JMB.2009.03.011 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0057 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6939 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 + TEST SET) : 0.288 REMARK 3 R VALUE (WORKING SET) : 0.285 REMARK 3 FREE R VALUE : 0.353 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 366 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 492 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4500 REMARK 3 BIN FREE R VALUE SET COUNT : 26 REMARK 3 BIN FREE R VALUE : 0.4730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2618 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.82000 REMARK 3 B12 (A**2) : -0.27000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.732 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.840 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 113.939 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.881 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2690 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3649 ; 2.253 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 322 ; 9.214 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;43.115 ;25.556 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 451 ;22.356 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;14.072 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 412 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2014 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1612 ; 0.902 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2629 ; 1.710 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1078 ; 2.007 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1020 ; 3.613 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 210 REMARK 3 ORIGIN FOR THE GROUP (A): -33.3030 2.9250 5.8120 REMARK 3 T TENSOR REMARK 3 T11: 0.1323 T22: 0.3571 REMARK 3 T33: 0.1418 T12: 0.0493 REMARK 3 T13: -0.0392 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 2.6238 L22: 2.4868 REMARK 3 L33: 1.8097 L12: -1.0982 REMARK 3 L13: -0.9551 L23: -0.5154 REMARK 3 S TENSOR REMARK 3 S11: 0.0472 S12: 0.1388 S13: 0.2183 REMARK 3 S21: -0.1131 S22: -0.0175 S23: 0.2229 REMARK 3 S31: -0.3612 S32: -0.3921 S33: -0.0297 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 211 A 326 REMARK 3 ORIGIN FOR THE GROUP (A): -15.5530 -8.8090 11.4790 REMARK 3 T TENSOR REMARK 3 T11: -0.0160 T22: 0.0286 REMARK 3 T33: -0.0501 T12: -0.0227 REMARK 3 T13: 0.0352 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 7.0662 L22: 6.1429 REMARK 3 L33: 6.2190 L12: -0.3590 REMARK 3 L13: -0.9189 L23: 0.3032 REMARK 3 S TENSOR REMARK 3 S11: 0.1513 S12: -0.9266 S13: -0.0702 REMARK 3 S21: 0.9243 S22: -0.3093 S23: -0.2010 REMARK 3 S31: 0.5227 S32: 0.2809 S33: 0.1579 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3FNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000050819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7350 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.88500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: 1SME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 20000, 0.1M TRIS-HCL PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 105.80000 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 52.90000 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 52.90000 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 105.80000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: ONE MOLECULE OF HISTO-ASPARTIC PROTEASE (HAP) IS PRESENT IN REMARK 300 THE ASYMMETRIC UNIT. ONE PEPSTATIN A MOLECULE IS BOUND TO THE REMARK 300 ACTIVE SITE OF THE ENZYME 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.90000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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: I 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 SER A -5 REMARK 465 TYR A -4 REMARK 465 LEU A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 GLU A 0 REMARK 465 PHE A 1 REMARK 465 ASN A 327 REMARK 465 LEU A 328 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 VAL A 312 N GLY A 321 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 126 NZ LYS A 162 4455 0.97 REMARK 500 NZ LYS A 126 CE LYS A 162 4455 1.85 REMARK 500 CE LYS A 126 NZ LYS A 162 4455 1.93 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 2 N ASP A 2 CA 0.121 REMARK 500 SER A 14 CA SER A 14 CB 0.108 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 ILE A 107 CB - CA - C ANGL. DEV. = -13.3 DEGREES REMARK 500 LEU A 128 CA - CB - CG ANGL. DEV. = 22.5 DEGREES REMARK 500 LEU A 214 CA - CB - CG ANGL. DEV. = -14.3 DEGREES REMARK 500 PRO A 241 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 PRO A 256 C - N - CA ANGL. DEV. = 9.4 DEGREES REMARK 500 LEU A 281 CA - CB - CG ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG A 307 NE - CZ - NH1 ANGL. DEV. = 4.5 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 LEU A 9 -70.04 -103.89 REMARK 500 ASN A 11 44.54 36.86 REMARK 500 SER A 14 79.63 -154.52 REMARK 500 SER A 36 -63.74 -92.42 REMARK 500 GLU A 51 -57.63 -29.20 REMARK 500 TYR A 64 102.30 -49.93 REMARK 500 ASP A 67 -49.82 -133.56 REMARK 500 ASP A 68 26.50 48.06 REMARK 500 LYS A 72 72.84 -111.19 REMARK 500 PRO A 98 105.38 -57.83 REMARK 500 VAL A 108 -74.06 -132.78 REMARK 500 SER A 132 59.42 37.27 REMARK 500 GLU A 139 57.75 -95.81 REMARK 500 LEU A 140 -25.10 -143.94 REMARK 500 ASN A 144 107.84 -43.50 REMARK 500 LYS A 160 -46.10 -131.06 REMARK 500 ASN A 161 -166.95 -78.19 REMARK 500 TRP A 190 72.15 -66.45 REMARK 500 PHE A 199 -84.49 -116.30 REMARK 500 PRO A 224 150.68 -43.29 REMARK 500 ALA A 235 67.37 -63.38 REMARK 500 PHE A 238 -162.97 -127.66 REMARK 500 SER A 243A 87.13 -68.12 REMARK 500 PRO A 263 3.90 -57.69 REMARK 500 GLU A 278A 28.93 -72.24 REMARK 500 ASN A 279 -125.02 52.83 REMARK 500 ASN A 285 43.01 -106.93 REMARK 500 GLU A 292 -160.00 173.95 REMARK 500 VAL I 2 88.19 17.87 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 I 4 ALA I 5 148.91 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 I 4 -14.50 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 RESIDUE EDO A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FNS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HISTO-ASPARTIC PROTEASE (HAP) FROM PLASMODIUM REMARK 900 FALCIPARUM REMARK 900 RELATED ID: 3FNU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KNI-10006 BOUND HISTO-ASPARTIC PROTEASE (HAP) REMARK 900 FROM PLASMODIUM FALCIPARUM DBREF 3FNT A -5 328 UNP Q8IM15 Q8IM15_PLAF7 120 451 DBREF 3FNT I 1 6 PDB 3FNT 3FNT 1 6 SEQRES 1 A 332 SER TYR LEU GLY SER GLU PHE ASP ASN VAL GLU LEU LYS SEQRES 2 A 332 ASP LEU ALA ASN VAL LEU SER PHE GLY GLU ALA LYS LEU SEQRES 3 A 332 GLY ASP ASN GLY GLN LYS PHE ASN PHE LEU PHE HIS THR SEQRES 4 A 332 ALA SER SER ASN VAL TRP VAL PRO SER ILE LYS CYS THR SEQRES 5 A 332 SER GLU SER CYS GLU SER LYS ASN HIS TYR ASP SER SER SEQRES 6 A 332 LYS SER LYS THR TYR GLU LYS ASP ASP THR PRO VAL LYS SEQRES 7 A 332 LEU THR SER LYS ALA GLY THR ILE SER GLY ILE PHE SER SEQRES 8 A 332 LYS ASP LEU VAL THR ILE GLY LYS LEU SER VAL PRO TYR SEQRES 9 A 332 LYS PHE ILE GLU MET THR GLU ILE VAL GLY PHE GLU PRO SEQRES 10 A 332 PHE TYR SER GLU SER ASP VAL ASP GLY VAL PHE GLY LEU SEQRES 11 A 332 GLY TRP LYS ASP LEU SER ILE GLY SER ILE ASP PRO TYR SEQRES 12 A 332 ILE VAL GLU LEU LYS THR GLN ASN LYS ILE GLU GLN ALA SEQRES 13 A 332 VAL TYR SER ILE TYR LEU PRO PRO GLU ASN LYS ASN LYS SEQRES 14 A 332 GLY TYR LEU THR ILE GLY GLY ILE GLU GLU ARG PHE PHE SEQRES 15 A 332 ASP GLY PRO LEU ASN TYR GLU LYS LEU ASN HIS ASP LEU SEQRES 16 A 332 MET TRP GLN VAL ASP LEU ASP VAL HIS PHE GLY ASN VAL SEQRES 17 A 332 SER SER LYS LYS ALA ASN VAL ILE LEU ASP SER ALA THR SEQRES 18 A 332 SER VAL ILE THR VAL PRO THR GLU PHE PHE ASN GLN PHE SEQRES 19 A 332 VAL GLU SER ALA SER VAL PHE LYS VAL PRO PHE LEU SER SEQRES 20 A 332 LEU TYR VAL THR THR CYS GLY ASN THR LYS LEU PRO THR SEQRES 21 A 332 LEU GLU TYR ARG SER PRO ASN LYS VAL TYR THR LEU GLU SEQRES 22 A 332 PRO LYS GLN TYR LEU GLU PRO LEU GLU ASN ILE PHE SER SEQRES 23 A 332 ALA LEU CYS MET LEU ASN ILE VAL PRO ILE ASP LEU GLU SEQRES 24 A 332 LYS ASN THR PHE VAL LEU GLY ASP PRO PHE MET ARG LYS SEQRES 25 A 332 TYR PHE THR VAL TYR ASP TYR ASP ASN HIS THR VAL GLY SEQRES 26 A 332 PHE ALA LEU ALA LYS ASN LEU SEQRES 1 I 6 IVA VAL VAL STA ALA STA HET IVA I 1 6 HET STA I 4 11 HET STA I 6 12 HET EDO A 501 4 HET EDO A 502 4 HETNAM IVA ISOVALERIC ACID HETNAM STA STATINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 IVA C5 H10 O2 FORMUL 2 STA 2(C8 H17 N O3) FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *9(H2 O) HELIX 1 1 SER A 47 LYS A 53 5 7 HELIX 2 2 PRO A 110 SER A 115 1 6 HELIX 3 3 PRO A 135 GLU A 139 5 5 HELIX 4 4 PRO A 224 GLU A 233 1 10 HELIX 5 5 GLU A 270 GLN A 273 5 4 HELIX 6 6 GLY A 302 ARG A 307 1 6 SHEET 1 A 5 ASN A 3 LEU A 6 0 SHEET 2 A 5 GLY A 163 ILE A 167 -1 O GLY A 163 N LEU A 6 SHEET 3 A 5 VAL A 150 TYR A 154 -1 N TYR A 154 O TYR A 164 SHEET 4 A 5 PHE A 310 ASP A 314 -1 O TYR A 313 N TYR A 151 SHEET 5 A 5 THR A 319 ALA A 323 -1 O GLY A 321 N VAL A 312 SHEET 1 B 8 GLU A 65 THR A 74 0 SHEET 2 B 8 THR A 79 THR A 90 -1 O ILE A 80 N LEU A 73 SHEET 3 B 8 PRO A 98 ILE A 107 -1 O GLU A 103 N ILE A 83 SHEET 4 B 8 TRP A 39 PRO A 41 1 N VAL A 40 O MET A 104 SHEET 5 B 8 GLY A 119 GLY A 122 -1 O VAL A 120 N TRP A 39 SHEET 6 B 8 GLN A 25 HIS A 32 1 N ASN A 28 O GLY A 119 SHEET 7 B 8 GLY A 16 LEU A 20 -1 N GLY A 16 O PHE A 29 SHEET 8 B 8 THR A 79 THR A 90 -1 O THR A 90 N LYS A 19 SHEET 1 C 5 TYR A 267 LEU A 269 0 SHEET 2 C 5 LEU A 258 ARG A 261 -1 N LEU A 258 O LEU A 269 SHEET 3 C 5 GLN A 191 HIS A 198 -1 N HIS A 198 O GLU A 259 SHEET 4 C 5 SER A 206 LEU A 214 -1 O ALA A 210 N LEU A 194 SHEET 5 C 5 THR A 298 LEU A 301 1 O LEU A 301 N ILE A 213 SHEET 1 D 2 ILE A 221 VAL A 223 0 SHEET 2 D 2 ILE A 286 PRO A 288 1 O VAL A 287 N VAL A 223 SHEET 1 E 4 PHE A 238 VAL A 240 0 SHEET 2 E 4 LEU A 243 THR A 248 -1 O VAL A 246 N PHE A 238 SHEET 3 E 4 LEU A 281 LEU A 284 -1 O CYS A 282 N THR A 247 SHEET 4 E 4 LEU A 275 PRO A 277 -1 N GLU A 276 O MET A 283 SSBOND 1 CYS A 45 CYS A 50 1555 1555 2.01 SSBOND 2 CYS A 249 CYS A 282 1555 1555 2.03 LINK C IVA I 1 N VAL I 2 1555 1555 1.34 LINK C VAL I 3 N STA I 4 1555 1555 1.25 LINK C STA I 4 N ALA I 5 1555 1555 1.34 LINK C ALA I 5 N STA I 6 1555 1555 1.38 CISPEP 1 GLU A 109B PRO A 110 0 3.47 SITE 1 AC1 4 ASN A 3 ASP A 127 SER A 129 SER A 132 CRYST1 70.700 70.700 158.700 90.00 90.00 120.00 P 32 2 1 6 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 0.014138 0.008163 0.000000 0.00000 SCALE2 0.000000 0.016325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006302 0.00000