HEADER HYDROLASE 04-OCT-17 5YIE TITLE CRYSTAL STRUCTURE OF KNI-10742 BOUND PLASMEPSIN II (PMII) FROM TITLE 2 PLASMODIUM FALCIPARUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMEPSIN II; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 127-453; COMPND 5 EC: 3.4.23.39; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_COMMON: ISOLATE 3D7; SOURCE 4 ORGANISM_TAXID: 36329; SOURCE 5 GENE: PF14_0077, PF3D7_1408000; SOURCE 6 EXPRESSION_SYSTEM: ENTEROBACTERIA PHAGE L1; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 268588 KEYWDS PLASMEPSIN, PLASMEPSIN II, KNI-10742, ASPARTIC PROTEASE, PLASMODIUM KEYWDS 2 FALCIPARUM, DRUG DEVELOPMENT, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.MISHRA,I.RATHORE,P.BHAUMIK REVDAT 3 29-MAY-19 5YIE 1 JRNL REVDAT 2 18-JUL-18 5YIE 1 JRNL REVDAT 1 11-JUL-18 5YIE 0 JRNL AUTH V.MISHRA,I.RATHORE,A.AREKAR,L.K.STHANAM,H.XIAO,Y.KISO,S.SEN, JRNL AUTH 2 S.PATANKAR,A.GUSTCHINA,K.HIDAKA,A.WLODAWER,R.Y.YADA, JRNL AUTH 3 P.BHAUMIK JRNL TITL DECIPHERING THE MECHANISM OF POTENT PEPTIDOMIMETIC JRNL TITL 2 INHIBITORS TARGETING PLASMEPSINS - BIOCHEMICAL AND JRNL TITL 3 STRUCTURAL INSIGHTS. JRNL REF FEBS J. V. 285 3077 2018 JRNL REFN ISSN 1742-464X JRNL PMID 29943906 JRNL DOI 10.1111/FEBS.14598 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22516 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1185 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1654 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2594 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.76 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) : 0.00000 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): 0.189 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.825 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2823 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2635 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3873 ; 1.750 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6103 ; 0.981 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 6.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;40.505 ;25.680 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 441 ;15.221 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;21.093 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3126 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 622 ; 0.002 ; 0.020 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): 1323 ; 1.512 ; 3.340 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1322 ; 1.513 ; 3.339 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1657 ; 2.425 ; 5.002 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1658 ; 2.424 ; 5.004 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1500 ; 2.121 ; 3.794 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1501 ; 2.121 ; 3.798 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2214 ; 3.519 ; 5.625 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3077 ; 6.596 ;28.285 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3045 ; 6.575 ;28.079 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 : 3 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 5 A 31 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1550 -40.3130 -12.5520 REMARK 3 T TENSOR REMARK 3 T11: 0.7779 T22: 0.3364 REMARK 3 T33: 0.5701 T12: 0.2200 REMARK 3 T13: 0.2568 T23: 0.2825 REMARK 3 L TENSOR REMARK 3 L11: 8.3766 L22: 0.3460 REMARK 3 L33: 4.4373 L12: 0.6162 REMARK 3 L13: 4.0573 L23: -0.3620 REMARK 3 S TENSOR REMARK 3 S11: -0.1148 S12: -0.4877 S13: -0.8351 REMARK 3 S21: 0.1087 S22: 0.1110 S23: 0.0064 REMARK 3 S31: 0.3709 S32: -0.0284 S33: 0.0038 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 32 A 211 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5260 -36.2100 -21.7390 REMARK 3 T TENSOR REMARK 3 T11: 0.2983 T22: 0.0503 REMARK 3 T33: 0.2069 T12: 0.0848 REMARK 3 T13: 0.0323 T23: 0.0523 REMARK 3 L TENSOR REMARK 3 L11: 3.7356 L22: 2.1245 REMARK 3 L33: 2.4301 L12: -1.5945 REMARK 3 L13: 0.8900 L23: -0.0764 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: 0.0728 S13: -0.4979 REMARK 3 S21: 0.1549 S22: -0.0975 S23: 0.1054 REMARK 3 S31: 0.6450 S32: 0.2798 S33: 0.0896 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 212 A 331 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4140 -24.9760 -24.3750 REMARK 3 T TENSOR REMARK 3 T11: 0.1295 T22: 0.0582 REMARK 3 T33: 0.2504 T12: -0.0296 REMARK 3 T13: 0.0188 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 2.6651 L22: 2.7668 REMARK 3 L33: 2.1253 L12: -1.8643 REMARK 3 L13: -0.6808 L23: 0.7530 REMARK 3 S TENSOR REMARK 3 S11: 0.0343 S12: 0.2350 S13: -0.5850 REMARK 3 S21: -0.0070 S22: -0.1120 S23: 0.4802 REMARK 3 S31: 0.3160 S32: -0.2406 S33: 0.0776 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54182 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 1.4 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 53.30000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.30000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 36.10000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.30000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.10000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 53.30000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 36.10000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 53.30000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 36.10000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 HOH A 529 O HOH A 628 2.19 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 ASP A 109 CB - CG - OD1 ANGL. DEV. = 5.4 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 ASN A 15 25.95 47.98 REMARK 500 LYS A 165 -48.67 -147.98 REMARK 500 SER A 220 38.89 -95.04 REMARK 500 PHE A 243 -2.73 74.07 REMARK 500 PRO A 245 39.27 -84.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CPS A 402 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 36 OD1 REMARK 620 2 ASP A 216 OD2 137.1 REMARK 620 3 8VF A 403 O23 83.2 127.9 REMARK 620 4 8VF A 403 O26 64.9 102.2 60.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8VF A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 DBREF 5YIE A 5 331 UNP Q8I6V3 Q8I6V3_PLAF7 127 453 SEQRES 1 A 327 ASN ASP ASN ILE GLU LEU VAL ASP PHE GLN ASN ILE MET SEQRES 2 A 327 PHE TYR GLY ASP ALA GLU VAL GLY ASP ASN GLN GLN PRO SEQRES 3 A 327 PHE THR PHE ILE LEU ASP THR GLY SER ALA ASN LEU TRP SEQRES 4 A 327 VAL PRO SER VAL LYS CYS THR THR ALA GLY CYS LEU THR SEQRES 5 A 327 LYS HIS LEU TYR ASP SER SER LYS SER ARG THR TYR GLU SEQRES 6 A 327 LYS ASP GLY THR LYS VAL GLU MET ASN TYR VAL SER GLY SEQRES 7 A 327 THR VAL SER GLY PHE PHE SER LYS ASP LEU VAL THR VAL SEQRES 8 A 327 GLY ASN LEU SER LEU PRO TYR LYS PHE ILE GLU VAL ILE SEQRES 9 A 327 ASP THR ASN GLY PHE GLU PRO THR TYR THR ALA SER THR SEQRES 10 A 327 PHE ASP GLY ILE LEU GLY LEU GLY TRP LYS ASP LEU SER SEQRES 11 A 327 ILE GLY SER VAL ASP PRO ILE VAL VAL GLU LEU LYS ASN SEQRES 12 A 327 GLN ASN LYS ILE GLU ASN ALA LEU PHE THR PHE TYR LEU SEQRES 13 A 327 PRO VAL HIS ASP LYS HIS THR GLY PHE LEU THR ILE GLY SEQRES 14 A 327 GLY ILE GLU GLU ARG PHE TYR GLU GLY PRO LEU THR TYR SEQRES 15 A 327 GLU LYS LEU ASN HIS ASP LEU TYR TRP GLN ILE THR LEU SEQRES 16 A 327 ASP ALA HIS VAL GLY ASN ILE MET LEU GLU LYS ALA ASN SEQRES 17 A 327 CYS ILE VAL ASP SER GLY THR SER ALA ILE THR VAL PRO SEQRES 18 A 327 THR ASP PHE LEU ASN LYS MET LEU GLN ASN LEU ASP VAL SEQRES 19 A 327 ILE LYS VAL PRO PHE LEU PRO PHE TYR VAL THR LEU CYS SEQRES 20 A 327 ASN ASN SER LYS LEU PRO THR PHE GLU PHE THR SER GLU SEQRES 21 A 327 ASN GLY LYS TYR THR LEU GLU PRO GLU TYR TYR LEU GLN SEQRES 22 A 327 HIS ILE GLU ASP VAL GLY PRO GLY LEU CYS MET LEU ASN SEQRES 23 A 327 ILE ILE GLY LEU ASP PHE PRO VAL PRO THR PHE ILE LEU SEQRES 24 A 327 GLY ASP PRO PHE MET ARG LYS TYR PHE THR VAL PHE ASP SEQRES 25 A 327 TYR ASP ASN GLN SER VAL GLY ILE ALA LEU ALA LYS LYS SEQRES 26 A 327 ASN LEU HET CPS A 401 42 HET CPS A 402 24 HET 8VF A 403 51 HET NA A 404 1 HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM 8VF (4R)-3-[(2S,3S)-3-[2-[4-[2-AZANYLETHYL(ETHYL)AMINO]-2, HETNAM 2 8VF 6-DIMETHYL-PHENOXY]ETHANOYLAMINO]-2-OXIDANYL-4-PHENYL- HETNAM 3 8VF BUTANOYL]-5,5-DIMETHYL-N-[(1S,2R)-2-OXIDANYL-2,3- HETNAM 4 8VF DIHYDRO-1H-INDEN-1-YL]-1,3-THIAZOLIDINE-4-CARBOXAMIDE HETNAM NA SODIUM ION HETSYN CPS CHAPS FORMUL 2 CPS 2(C32 H58 N2 O7 S) FORMUL 4 8VF C39 H51 N5 O6 S FORMUL 5 NA NA 1+ FORMUL 6 HOH *142(H2 O) HELIX 1 AA1 THR A 51 LYS A 57 5 7 HELIX 2 AA2 ASP A 61 SER A 65 5 5 HELIX 3 AA3 THR A 110 GLU A 114 5 5 HELIX 4 AA4 PRO A 115 SER A 120 1 6 HELIX 5 AA5 TRP A 130 SER A 134 5 5 HELIX 6 AA6 PRO A 140 GLN A 148 1 9 HELIX 7 AA7 GLU A 176 ARG A 178 5 3 HELIX 8 AA8 PRO A 225 GLN A 234 1 10 HELIX 9 AA9 GLU A 271 TYR A 275 1 5 HELIX 10 AB1 GLY A 304 LYS A 310 1 7 SHEET 1 AA1 9 GLU A 69 TYR A 79 0 SHEET 2 AA1 9 GLY A 82 VAL A 95 -1 O VAL A 84 N MET A 77 SHEET 3 AA1 9 MET A 17 VAL A 24 -1 N GLU A 23 O THR A 94 SHEET 4 AA1 9 ASP A 6 PHE A 13 -1 N PHE A 13 O MET A 17 SHEET 5 AA1 9 GLY A 168 ILE A 172 -1 O LEU A 170 N ILE A 8 SHEET 6 AA1 9 LEU A 155 TYR A 159 -1 N TYR A 159 O PHE A 169 SHEET 7 AA1 9 TYR A 311 ASP A 316 -1 O PHE A 315 N PHE A 156 SHEET 8 AA1 9 SER A 321 ALA A 327 -1 O GLY A 323 N VAL A 314 SHEET 9 AA1 9 TYR A 180 LYS A 188 -1 N GLU A 181 O LEU A 326 SHEET 1 AA213 GLU A 69 TYR A 79 0 SHEET 2 AA213 GLY A 82 VAL A 95 -1 O VAL A 84 N MET A 77 SHEET 3 AA213 LEU A 98 ASP A 109 -1 O GLU A 106 N PHE A 87 SHEET 4 AA213 LEU A 42 PRO A 45 1 N VAL A 44 O VAL A 107 SHEET 5 AA213 GLY A 124 GLY A 127 -1 O ILE A 125 N TRP A 43 SHEET 6 AA213 PRO A 30 ASP A 36 1 N ILE A 34 O LEU A 126 SHEET 7 AA213 MET A 17 VAL A 24 -1 N GLY A 20 O PHE A 33 SHEET 8 AA213 ASP A 6 PHE A 13 -1 N PHE A 13 O MET A 17 SHEET 9 AA213 GLY A 168 ILE A 172 -1 O LEU A 170 N ILE A 8 SHEET 10 AA213 LEU A 155 TYR A 159 -1 N TYR A 159 O PHE A 169 SHEET 11 AA213 TYR A 311 ASP A 316 -1 O PHE A 315 N PHE A 156 SHEET 12 AA213 SER A 321 ALA A 327 -1 O GLY A 323 N VAL A 314 SHEET 13 AA213 TYR A 180 LYS A 188 -1 N GLU A 181 O LEU A 326 SHEET 1 AA3 7 LYS A 267 LEU A 270 0 SHEET 2 AA3 7 PHE A 259 THR A 262 -1 N PHE A 261 O TYR A 268 SHEET 3 AA3 7 GLN A 196 VAL A 203 -1 N HIS A 202 O GLU A 260 SHEET 4 AA3 7 ILE A 206 VAL A 215 -1 O CYS A 213 N ILE A 197 SHEET 5 AA3 7 THR A 300 LEU A 303 1 O LEU A 303 N ILE A 214 SHEET 6 AA3 7 ILE A 222 VAL A 224 -1 N THR A 223 O ILE A 302 SHEET 7 AA3 7 ILE A 291 GLY A 293 1 O ILE A 292 N VAL A 224 SHEET 1 AA4 4 ILE A 239 LYS A 240 0 SHEET 2 AA4 4 TYR A 247 LEU A 250 -1 O VAL A 248 N ILE A 239 SHEET 3 AA4 4 LEU A 286 LEU A 289 -1 O CYS A 287 N THR A 249 SHEET 4 AA4 4 LEU A 276 HIS A 278 -1 N GLN A 277 O MET A 288 SSBOND 1 CYS A 49 CYS A 54 1555 1555 2.04 SSBOND 2 CYS A 251 CYS A 287 1555 1555 2.09 LINK OD1 ASP A 36 NA NA A 404 1555 1555 2.64 LINK OD2BASP A 216 NA NA A 404 1555 1555 1.99 LINK O23 8VF A 403 NA NA A 404 1555 1555 2.74 LINK O26 8VF A 403 NA NA A 404 1555 1555 2.30 CISPEP 1 GLU A 114 PRO A 115 0 9.61 SITE 1 AC1 10 VAL A 80 PRO A 115 SER A 254 LYS A 255 SITE 2 AC1 10 LEU A 256 ILE A 292 CPS A 402 8VF A 403 SITE 3 AC1 10 HOH A 512 HOH A 576 SITE 1 AC2 6 VAL A 80 LEU A 294 ASP A 295 CPS A 401 SITE 2 AC2 6 8VF A 403 HOH A 550 SITE 1 AC3 20 ILE A 34 ASP A 36 GLY A 38 LEU A 55 SITE 2 AC3 20 TYR A 79 VAL A 80 SER A 81 LEU A 133 SITE 3 AC3 20 ILE A 135 ASP A 216 GLY A 218 THR A 219 SITE 4 AC3 20 SER A 220 ILE A 292 LEU A 294 ILE A 302 SITE 5 AC3 20 CPS A 401 CPS A 402 NA A 404 HOH A 526 SITE 1 AC4 6 ASP A 36 GLY A 38 ASP A 216 GLY A 218 SITE 2 AC4 6 THR A 219 8VF A 403 CRYST1 106.600 106.600 72.200 90.00 90.00 90.00 I 4 8 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 0.009381 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013850 0.00000