HEADER HYDROLASE 03-OCT-17 5YIC TITLE CRYSTAL STRUCTURE OF KNI-10333 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 126-453; COMPND 5 EC: 3.4.23.39; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; 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-10333, ASPARTIC PROTEASE, PLASMODIUM KEYWDS 2 FALCIPARUM, DRUG DEVELOPMENT, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.MISHRA,I.RATHORE,P.BHAUMIK REVDAT 4 06-NOV-24 5YIC 1 REMARK REVDAT 3 29-MAY-19 5YIC 1 JRNL REVDAT 2 18-JUL-18 5YIC 1 JRNL REVDAT 1 11-JUL-18 5YIC 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. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 29718 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1565 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2182 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.4000 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2600 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.24000 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): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.929 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2831 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2637 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3872 ; 1.661 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6107 ; 0.968 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 341 ; 6.624 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;39.528 ;25.528 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 444 ;15.168 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;20.396 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3144 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 636 ; 0.003 ; 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): 1331 ; 1.310 ; 2.936 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1330 ; 1.308 ; 2.935 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1668 ; 2.062 ; 4.395 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1669 ; 2.062 ; 4.396 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1500 ; 1.806 ; 3.298 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1500 ; 1.805 ; 3.298 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2200 ; 2.882 ; 4.860 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3242 ; 7.456 ;25.965 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3243 ; 7.457 ;25.970 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 : 4 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 4 A 31 REMARK 3 ORIGIN FOR THE GROUP (A): -40.2336 17.3810 -22.6521 REMARK 3 T TENSOR REMARK 3 T11: 0.1886 T22: 0.4165 REMARK 3 T33: 0.2914 T12: 0.0862 REMARK 3 T13: -0.1167 T23: -0.0950 REMARK 3 L TENSOR REMARK 3 L11: 0.8187 L22: 4.6187 REMARK 3 L33: 4.3281 L12: 0.5875 REMARK 3 L13: 0.9901 L23: -2.4611 REMARK 3 S TENSOR REMARK 3 S11: 0.1165 S12: 0.2250 S13: -0.0814 REMARK 3 S21: -0.4121 S22: -0.0650 S23: 0.2403 REMARK 3 S31: 0.2890 S32: 0.0547 S33: -0.0515 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 140 REMARK 3 ORIGIN FOR THE GROUP (A): -33.9657 28.4319 -18.2418 REMARK 3 T TENSOR REMARK 3 T11: 0.0529 T22: 0.0892 REMARK 3 T33: 0.1305 T12: 0.0341 REMARK 3 T13: -0.0431 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.2982 L22: 2.8422 REMARK 3 L33: 2.0128 L12: -0.4686 REMARK 3 L13: 0.2067 L23: -1.1250 REMARK 3 S TENSOR REMARK 3 S11: -0.0238 S12: 0.1676 S13: 0.1359 REMARK 3 S21: -0.0651 S22: -0.0720 S23: 0.0086 REMARK 3 S31: -0.2417 S32: -0.1701 S33: 0.0958 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 141 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): -39.1244 9.3341 -6.4416 REMARK 3 T TENSOR REMARK 3 T11: 0.0296 T22: 0.1377 REMARK 3 T33: 0.2159 T12: -0.0366 REMARK 3 T13: 0.0609 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.7425 L22: 3.2103 REMARK 3 L33: 2.3610 L12: -1.5485 REMARK 3 L13: 0.5870 L23: -0.3710 REMARK 3 S TENSOR REMARK 3 S11: -0.1167 S12: -0.0205 S13: -0.3071 REMARK 3 S21: 0.1632 S22: 0.0937 S23: 0.5036 REMARK 3 S31: 0.1072 S32: -0.3007 S33: 0.0230 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 214 A 331 REMARK 3 ORIGIN FOR THE GROUP (A): -24.9818 2.1908 -11.0861 REMARK 3 T TENSOR REMARK 3 T11: 0.0411 T22: 0.0578 REMARK 3 T33: 0.2067 T12: -0.0259 REMARK 3 T13: -0.0053 T23: -0.0243 REMARK 3 L TENSOR REMARK 3 L11: 1.8249 L22: 1.5641 REMARK 3 L33: 1.4666 L12: -1.3676 REMARK 3 L13: -0.7491 L23: 0.5828 REMARK 3 S TENSOR REMARK 3 S11: -0.0389 S12: 0.0497 S13: -0.3106 REMARK 3 S21: 0.1116 S22: -0.0103 S23: 0.3191 REMARK 3 S31: 0.1465 S32: -0.1012 S33: 0.0492 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5YIC 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_1300005326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31284 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 : 5.300 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 1.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 54.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 1.26 M AMMONIUM REMARK 280 SULFATE, 0.1 M TRIS PH 8.5, 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 53.25000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.25000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.50000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.25000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.25000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.50000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 53.25000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 53.25000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.50000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 53.25000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 53.25000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.50000 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: 320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 O HOH A 678 O HOH A 678 2455 2.04 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 GLU A 177 CD GLU A 177 OE1 0.080 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 17.17 52.08 REMARK 500 ALA A 40 26.65 -141.48 REMARK 500 ASP A 71 -73.49 -123.98 REMARK 500 HIS A 163 123.95 -39.99 REMARK 500 LYS A 165 -51.67 -141.43 REMARK 500 LEU A 193 20.12 -140.57 REMARK 500 SER A 220 48.81 -92.85 REMARK 500 SER A 220 59.04 -93.83 REMARK 500 PRO A 245 39.96 -85.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 750 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 751 DISTANCE = 6.63 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8VO 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 GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 DBREF 5YIC A 4 331 UNP Q8I6V3 Q8I6V3_PLAF7 126 453 SEQRES 1 A 328 SER ASN ASP ASN ILE GLU LEU VAL ASP PHE GLN ASN ILE SEQRES 2 A 328 MET PHE TYR GLY ASP ALA GLU VAL GLY ASP ASN GLN GLN SEQRES 3 A 328 PRO PHE THR PHE ILE LEU ASP THR GLY SER ALA ASN LEU SEQRES 4 A 328 TRP VAL PRO SER VAL LYS CYS THR THR ALA GLY CYS LEU SEQRES 5 A 328 THR LYS HIS LEU TYR ASP SER SER LYS SER ARG THR TYR SEQRES 6 A 328 GLU LYS ASP GLY THR LYS VAL GLU MET ASN TYR VAL SER SEQRES 7 A 328 GLY THR VAL SER GLY PHE PHE SER LYS ASP LEU VAL THR SEQRES 8 A 328 VAL GLY ASN LEU SER LEU PRO TYR LYS PHE ILE GLU VAL SEQRES 9 A 328 ILE ASP THR ASN GLY PHE GLU PRO THR TYR THR ALA SER SEQRES 10 A 328 THR PHE ASP GLY ILE LEU GLY LEU GLY TRP LYS ASP LEU SEQRES 11 A 328 SER ILE GLY SER VAL ASP PRO ILE VAL VAL GLU LEU LYS SEQRES 12 A 328 ASN GLN ASN LYS ILE GLU ASN ALA LEU PHE THR PHE TYR SEQRES 13 A 328 LEU PRO VAL HIS ASP LYS HIS THR GLY PHE LEU THR ILE SEQRES 14 A 328 GLY GLY ILE GLU GLU ARG PHE TYR GLU GLY PRO LEU THR SEQRES 15 A 328 TYR GLU LYS LEU ASN HIS ASP LEU TYR TRP GLN ILE THR SEQRES 16 A 328 LEU ASP ALA HIS VAL GLY ASN ILE MET LEU GLU LYS ALA SEQRES 17 A 328 ASN CYS ILE VAL ASP SER GLY THR SER ALA ILE THR VAL SEQRES 18 A 328 PRO THR ASP PHE LEU ASN LYS MET LEU GLN ASN LEU ASP SEQRES 19 A 328 VAL ILE LYS VAL PRO PHE LEU PRO PHE TYR VAL THR LEU SEQRES 20 A 328 CYS ASN ASN SER LYS LEU PRO THR PHE GLU PHE THR SER SEQRES 21 A 328 GLU ASN GLY LYS TYR THR LEU GLU PRO GLU TYR TYR LEU SEQRES 22 A 328 GLN HIS ILE GLU ASP VAL GLY PRO GLY LEU CYS MET LEU SEQRES 23 A 328 ASN ILE ILE GLY LEU ASP PHE PRO VAL PRO THR PHE ILE SEQRES 24 A 328 LEU GLY ASP PRO PHE MET ARG LYS TYR PHE THR VAL PHE SEQRES 25 A 328 ASP TYR ASP ASN GLN SER VAL GLY ILE ALA LEU ALA LYS SEQRES 26 A 328 LYS ASN LEU HET 8VO A 401 50 HET CPS A 402 42 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HETNAM 8VO (4R)-3-[(2S,3S)-3-[[(2R)-2-[2-(4-AMINOPHENYL) HETNAM 2 8VO ETHANOYLAMINO]-3-METHYLSULFANYL-PROPANOYL]AMINO]-2- HETNAM 3 8VO OXIDANYL-4-PHENYL-BUTANOYL]-5,5-DIMETHYL-N-[(1S,2R)-2- HETNAM 4 8VO OXIDANYL-2,3-DIHYDRO-1H-INDEN-1-YL]-1,3-THIAZOLIDINE- HETNAM 5 8VO 4-CARBOXAMIDE HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM GOL GLYCEROL HETSYN CPS CHAPS HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8VO C37 H45 N5 O6 S2 FORMUL 3 CPS C32 H58 N2 O7 S FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 HOH *251(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 LYS A 90 N GLU A 69 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 187 O VAL A 322 SHEET 1 AA213 GLU A 69 TYR A 79 0 SHEET 2 AA213 GLY A 82 VAL A 95 -1 O LYS A 90 N GLU A 69 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 GLN A 29 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 187 O VAL A 322 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 LEU A 208 N ALA A 201 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 ILE A 222 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 2.07 SSBOND 2 CYS A 251 CYS A 287 1555 1555 2.09 CISPEP 1 GLU A 114 PRO A 115 0 8.46 SITE 1 AC1 20 ASP A 36 GLY A 38 ASN A 78 TYR A 79 SITE 2 AC1 20 VAL A 80 SER A 81 LEU A 133 ASP A 216 SITE 3 AC1 20 GLY A 218 THR A 219 SER A 220 LEU A 294 SITE 4 AC1 20 ASP A 295 PHE A 296 ILE A 302 CPS A 402 SITE 5 AC1 20 GOL A 406 HOH A 514 HOH A 534 HOH A 631 SITE 1 AC2 16 VAL A 80 SER A 81 GLY A 204 PHE A 246 SITE 2 AC2 16 SER A 254 LYS A 255 PRO A 257 THR A 258 SITE 3 AC2 16 GLU A 260 ILE A 292 LEU A 294 8VO A 401 SITE 4 AC2 16 HOH A 509 HOH A 525 HOH A 558 HOH A 668 SITE 1 AC3 4 GLU A 181 GLY A 182 LYS A 328 HOH A 626 SITE 1 AC4 9 ASN A 235 LEU A 236 ASP A 237 LYS A 240 SITE 2 AC4 9 HOH A 513 HOH A 547 HOH A 552 HOH A 560 SITE 3 AC4 9 HOH A 567 SITE 1 AC5 4 LYS A 48 TYR A 68 LYS A 70 HOH A 537 SITE 1 AC6 5 GLY A 38 TYR A 194 ILE A 214 8VO A 401 SITE 2 AC6 5 HOH A 507 CRYST1 106.500 106.500 71.000 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 0.009390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014085 0.00000