HEADER HYDROLASE 03-OCT-17 5YIB TITLE CRYSTAL STRUCTURE OF KNI-10743 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-10743, ASPARTIC PROTEASE, PLASMODIUM KEYWDS 2 FALCIPARUM, DRUG DEVELOPMENT, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.RATHORE,V.MISHRA,P.BHAUMIK REVDAT 3 29-MAY-19 5YIB 1 JRNL REVDAT 2 18-JUL-18 5YIB 1 JRNL REVDAT 1 11-JUL-18 5YIB 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20484 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1078 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1519 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3640 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 : 121 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : -0.98000 REMARK 3 B33 (A**2) : 1.96000 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): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.802 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2817 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2627 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3840 ; 1.529 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6077 ; 0.938 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 6.921 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;39.821 ;25.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 441 ;15.859 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;24.711 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 434 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3117 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 629 ; 0.001 ; 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): 1319 ; 1.159 ; 2.922 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1318 ; 1.159 ; 2.921 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1649 ; 1.966 ; 4.378 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1650 ; 1.965 ; 4.379 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1498 ; 1.481 ; 3.286 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1499 ; 1.480 ; 3.288 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2188 ; 2.460 ; 4.830 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3010 ; 5.351 ;24.570 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3011 ; 5.351 ;24.582 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 4 A 17 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9486 -39.2140 -13.4602 REMARK 3 T TENSOR REMARK 3 T11: 0.2231 T22: 0.2296 REMARK 3 T33: 0.1628 T12: -0.0268 REMARK 3 T13: 0.0859 T23: 0.0429 REMARK 3 L TENSOR REMARK 3 L11: 4.4912 L22: 7.7720 REMARK 3 L33: 12.1643 L12: -3.4456 REMARK 3 L13: -3.0411 L23: 4.2874 REMARK 3 S TENSOR REMARK 3 S11: 0.1315 S12: -0.7101 S13: -0.1160 REMARK 3 S21: 0.5612 S22: 0.0874 S23: 0.2130 REMARK 3 S31: -0.3145 S32: -0.0832 S33: -0.2189 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 18 A 220 REMARK 3 ORIGIN FOR THE GROUP (A): 20.3843 -36.2623 -20.6624 REMARK 3 T TENSOR REMARK 3 T11: 0.1849 T22: 0.1005 REMARK 3 T33: 0.1043 T12: 0.0139 REMARK 3 T13: 0.0350 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 2.8217 L22: 1.6096 REMARK 3 L33: 1.5778 L12: -0.7424 REMARK 3 L13: 1.0318 L23: -0.1433 REMARK 3 S TENSOR REMARK 3 S11: -0.0159 S12: -0.0347 S13: -0.2054 REMARK 3 S21: 0.1138 S22: -0.0501 S23: 0.0574 REMARK 3 S31: 0.1536 S32: 0.1171 S33: 0.0660 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 221 A 331 REMARK 3 ORIGIN FOR THE GROUP (A): 1.6124 -25.1126 -23.7880 REMARK 3 T TENSOR REMARK 3 T11: 0.0879 T22: 0.0945 REMARK 3 T33: 0.1831 T12: -0.0144 REMARK 3 T13: 0.0167 T23: 0.0237 REMARK 3 L TENSOR REMARK 3 L11: 1.8864 L22: 2.7846 REMARK 3 L33: 1.5047 L12: -1.2992 REMARK 3 L13: -0.6996 L23: 0.9035 REMARK 3 S TENSOR REMARK 3 S11: 0.0692 S12: 0.1206 S13: -0.3024 REMARK 3 S21: 0.0265 S22: -0.1032 S23: 0.4402 REMARK 3 S31: 0.0470 S32: -0.1530 S33: 0.0340 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 5YIB 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_1300005324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-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) : 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 : 21566 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.99000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 54.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 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 53.12500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.12500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.42500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.12500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.12500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.42500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 53.12500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 53.12500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.42500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 53.12500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 53.12500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.42500 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: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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: 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 4.51 54.29 REMARK 500 ASP A 71 -71.32 -123.70 REMARK 500 ASP A 164 -46.52 76.66 REMARK 500 SER A 220 34.12 -91.63 REMARK 500 PRO A 245 34.21 -84.55 REMARK 500 ASN A 253 107.71 -55.18 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 409 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8VC A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 409 DBREF 5YIB 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 8VC A 401 52 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET EDO A 407 4 HET EDO A 408 4 HET CPS A 409 31 HETNAM 8VC (4R)-3-[(2S,3S)-3-[2-[4-[2-(DIMETHYLAMINO)ETHYL-METHYL- HETNAM 2 8VC AMINO]-2,6-DIMETHYL-PHENOXY]ETHANOYLAMINO]-2-OXIDANYL- HETNAM 3 8VC 4-PHENYL-BUTANOYL]-5,5-DIMETHYL-N-[(1S,2R)-2-OXIDANYL- HETNAM 4 8VC 2,3-DIHYDRO-1H-INDEN-1-YL]-1,3-THIAZOLIDINE-4- HETNAM 5 8VC CARBOXAMIDE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL HETSYN CPS CHAPS FORMUL 2 8VC C40 H53 N5 O6 S FORMUL 3 GOL 5(C3 H8 O3) FORMUL 8 EDO 2(C2 H6 O2) FORMUL 10 CPS C32 H58 N2 O7 S FORMUL 11 HOH *114(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 ILE A 172 N ASP A 6 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 THR A 185 O ILE A 324 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 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 ILE A 172 N ASP A 6 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 THR A 185 O ILE A 324 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 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 2.06 SSBOND 2 CYS A 251 CYS A 287 1555 1555 2.09 CISPEP 1 GLU A 114 PRO A 115 0 5.97 SITE 1 AC1 18 ILE A 34 ASP A 36 GLY A 38 MET A 77 SITE 2 AC1 18 TYR A 79 VAL A 80 SER A 81 LEU A 133 SITE 3 AC1 18 SER A 134 ASP A 216 GLY A 218 THR A 219 SITE 4 AC1 18 SER A 220 ILE A 292 PHE A 296 ILE A 302 SITE 5 AC1 18 EDO A 407 CPS A 409 SITE 1 AC2 3 GLU A 181 GLY A 182 LYS A 328 SITE 1 AC3 3 SER A 220 MET A 288 ASN A 290 SITE 1 AC4 3 LYS A 48 TYR A 68 LYS A 70 SITE 1 AC5 7 ASN A 235 LEU A 236 ASP A 237 VAL A 238 SITE 2 AC5 7 LYS A 240 HOH A 503 HOH A 529 SITE 1 AC6 4 THR A 198 ASP A 200 SER A 263 GLU A 264 SITE 1 AC7 5 GLY A 38 TYR A 194 ILE A 214 8VC A 401 SITE 2 AC7 5 HOH A 549 SITE 1 AC8 3 THR A 269 LYS A 310 HOH A 557 SITE 1 AC9 8 VAL A 80 SER A 81 THR A 116 SER A 254 SITE 2 AC9 8 LYS A 255 LEU A 294 8VC A 401 HOH A 587 CRYST1 106.250 106.250 70.850 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 0.009412 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009412 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014114 0.00000