HEADER HYDROLASE 25-APR-17 5VLK TITLE SHORT PCSK9 DELTA-P' COMPLEX WITH SHRUNKEN PEPTIDE BEARING HOMO- TITLE 2 ARGININE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-452; COMPND 5 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1,NARC-1,PROPROTEIN COMPND 6 CONVERTASE 9,PC9,SUBTILISIN/KEXIN-LIKE PROTEASE PC9; COMPND 7 EC: 3.4.21.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: ACE-THR-VAL-PHE-THR-SER-TRP-GLU-GLU-TYR-LEU-ASP-TRP-VAL-NH2 COMPND 12 PEPTIDE; COMPND 13 CHAIN: Y; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: ACE-TRP-ASN-LEU-VAL-HRG-ILE-GLY-LEU-LEU PEPTIDE; COMPND 17 CHAIN: Z; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCSK9, NARC1, PSEC0052; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS PROPROTEIN CONVERTASE, SUBTILISIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.EIGENBROT,M.ULTSCH REVDAT 8 15-NOV-23 5VLK 1 LINK REVDAT 7 04-OCT-23 5VLK 1 LINK REVDAT 6 04-MAR-20 5VLK 1 COMPND SOURCE REMARK DBREF REVDAT 6 2 1 SEQRES LINK SITE ATOM REVDAT 5 04-DEC-19 5VLK 1 SOURCE REVDAT 4 18-OCT-17 5VLK 1 JRNL REVDAT 3 20-SEP-17 5VLK 1 REMARK REVDAT 2 06-SEP-17 5VLK 1 JRNL REVDAT 1 16-AUG-17 5VLK 0 JRNL AUTH Y.ZHANG,M.ULTSCH,N.J.SKELTON,D.J.BURDICK,M.H.BERESINI,W.LI, JRNL AUTH 2 M.KONG-BELTRAN,A.PETERSON,J.QUINN,C.CHIU,Y.WU,S.SHIA, JRNL AUTH 3 P.MORAN,P.DI LELLO,C.EIGENBROT,D.KIRCHHOFER JRNL TITL DISCOVERY OF A CRYPTIC PEPTIDE-BINDING SITE ON PCSK9 AND JRNL TITL 2 DESIGN OF ANTAGONISTS. JRNL REF NAT. STRUCT. MOL. BIOL. V. 24 848 2017 JRNL REFN ESSN 1545-9985 JRNL PMID 28825733 JRNL DOI 10.1038/NSMB.3453 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22615 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 981 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3216 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2869 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.80000 REMARK 3 B22 (A**2) : -0.80000 REMARK 3 B33 (A**2) : 2.60000 REMARK 3 B12 (A**2) : -0.40000 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): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.888 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2943 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2840 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3999 ; 1.260 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6515 ; 0.959 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 5.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;32.764 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;13.245 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.050 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 468 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3335 ; 0.021 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 659 ; 0.017 ; 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): 1516 ; 3.164 ; 5.104 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1515 ; 3.126 ; 5.098 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1883 ; 4.551 ;11.388 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1884 ; 4.550 ;11.399 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1427 ; 4.157 ; 5.942 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1428 ; 4.156 ; 5.948 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2114 ; 6.498 ;12.878 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3231 ; 7.907 ;36.480 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3191 ; 7.897 ;36.238 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 5VLK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23637 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11100 REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.86300 REMARK 200 FOR SHELL : 2.500 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: 4NMX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM ACETATE, PEG 6000, PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 104.65533 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 52.32767 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 52.32767 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 104.65533 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, Y, Z 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 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 THR A 3 REMARK 465 VAL A 4 REMARK 465 SER A 5 REMARK 465 SER A 6 REMARK 465 ARG A 7 REMARK 465 ARG A 8 REMARK 465 SER A 9 REMARK 465 TRP A 10 REMARK 465 TRP A 11 REMARK 465 PRO A 12 REMARK 465 LEU A 13 REMARK 465 PRO A 14 REMARK 465 LEU A 15 REMARK 465 LEU A 16 REMARK 465 LEU A 17 REMARK 465 LEU A 18 REMARK 465 LEU A 19 REMARK 465 LEU A 20 REMARK 465 LEU A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 GLY A 24 REMARK 465 PRO A 25 REMARK 465 ALA A 26 REMARK 465 GLY A 27 REMARK 465 ALA A 28 REMARK 465 ARG A 29 REMARK 465 ALA A 30 REMARK 465 GLN A 31 REMARK 465 GLU A 32 REMARK 465 ASP A 33 REMARK 465 GLU A 34 REMARK 465 ASP A 35 REMARK 465 GLY A 36 REMARK 465 ASP A 37 REMARK 465 TYR A 38 REMARK 465 GLU A 39 REMARK 465 GLU A 40 REMARK 465 LEU A 41 REMARK 465 VAL A 42 REMARK 465 LEU A 43 REMARK 465 ALA A 44 REMARK 465 LEU A 45 REMARK 465 ARG A 46 REMARK 465 SER A 47 REMARK 465 GLU A 48 REMARK 465 GLU A 49 REMARK 465 ASP A 50 REMARK 465 GLY A 51 REMARK 465 LEU A 52 REMARK 465 ALA A 53 REMARK 465 GLU A 54 REMARK 465 ALA A 55 REMARK 465 PRO A 56 REMARK 465 GLU A 57 REMARK 465 HIS A 58 REMARK 465 GLY A 59 REMARK 465 THR A 60 REMARK 465 SER A 153 REMARK 465 ILE A 154 REMARK 465 PRO A 155 REMARK 465 TRP A 156 REMARK 465 ASN A 157 REMARK 465 LEU A 158 REMARK 465 GLU A 159 REMARK 465 ARG A 160 REMARK 465 ILE A 161 REMARK 465 THR A 162 REMARK 465 PRO A 163 REMARK 465 PRO A 164 REMARK 465 ARG A 165 REMARK 465 TYR A 166 REMARK 465 SER A 167 REMARK 465 ALA A 168 REMARK 465 ASP A 169 REMARK 465 GLU A 170 REMARK 465 TYR A 171 REMARK 465 GLN A 172 REMARK 465 PRO A 173 REMARK 465 PRO A 174 REMARK 465 ASP A 175 REMARK 465 GLY A 213 REMARK 465 THR A 214 REMARK 465 ARG A 215 REMARK 465 PHE A 216 REMARK 465 HIS A 217 REMARK 465 ARG A 218 REMARK 465 GLN A 219 REMARK 465 ALA A 220 REMARK 465 SER A 447 REMARK 465 THR A 448 REMARK 465 HIS A 449 REMARK 465 GLY A 450 REMARK 465 ALA A 451 REMARK 465 GLY A 452 REMARK 465 ASN A 453 REMARK 465 SER A 454 REMARK 465 HIS A 455 REMARK 465 HIS A 456 REMARK 465 HIS A 457 REMARK 465 HIS A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 ARG Z 10 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 HIS A 113 137.50 -171.50 REMARK 500 LEU A 118 -64.54 -120.84 REMARK 500 HIS A 139 -2.57 77.47 REMARK 500 ASP A 186 -155.81 -163.59 REMARK 500 ASN A 254 -168.64 -79.11 REMARK 500 VAL A 280 -143.39 -128.82 REMARK 500 LEU A 351 -148.43 -109.19 REMARK 500 ASN A 425 97.69 -69.12 REMARK 500 REMARK 500 REMARK: NULL 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 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 331 O REMARK 620 2 VAL A 333 O 83.5 REMARK 620 3 ASP A 360 OD1 144.3 115.6 REMARK 620 4 ASP A 360 OD2 163.0 79.4 47.5 REMARK 620 5 HOH A 651 O 82.3 79.5 128.9 94.4 REMARK 620 6 HOH A 750 O 110.7 147.8 69.9 84.2 74.3 REMARK 620 7 HOH A 753 O 80.6 145.7 66.8 114.0 127.6 66.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VLH RELATED DB: PDB REMARK 900 RELATED ID: 5VL7 RELATED DB: PDB REMARK 900 RELATED ID: 5VLA RELATED DB: PDB REMARK 900 RELATED ID: 5VLL RELATED DB: PDB REMARK 900 RELATED ID: 5VLP RELATED DB: PDB DBREF 5VLK A 1 452 UNP Q8NBP7 PCSK9_HUMAN 1 452 DBREF 5VLK Y 0 14 PDB 5VLK 5VLK 0 14 DBREF 5VLK Z 0 10 PDB 5VLK 5VLK 0 10 SEQADV 5VLK SER A 167 UNP Q8NBP7 ARG 167 ENGINEERED MUTATION SEQADV 5VLK ASN A 453 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK SER A 454 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK HIS A 455 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK HIS A 456 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK HIS A 457 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK HIS A 458 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK HIS A 459 UNP Q8NBP7 EXPRESSION TAG SEQADV 5VLK HIS A 460 UNP Q8NBP7 EXPRESSION TAG SEQRES 1 A 460 MET GLY THR VAL SER SER ARG ARG SER TRP TRP PRO LEU SEQRES 2 A 460 PRO LEU LEU LEU LEU LEU LEU LEU LEU LEU GLY PRO ALA SEQRES 3 A 460 GLY ALA ARG ALA GLN GLU ASP GLU ASP GLY ASP TYR GLU SEQRES 4 A 460 GLU LEU VAL LEU ALA LEU ARG SER GLU GLU ASP GLY LEU SEQRES 5 A 460 ALA GLU ALA PRO GLU HIS GLY THR THR ALA THR PHE HIS SEQRES 6 A 460 ARG CYS ALA LYS ASP PRO TRP ARG LEU PRO GLY THR TYR SEQRES 7 A 460 VAL VAL VAL LEU LYS GLU GLU THR HIS LEU SER GLN SER SEQRES 8 A 460 GLU ARG THR ALA ARG ARG LEU GLN ALA GLN ALA ALA ARG SEQRES 9 A 460 ARG GLY TYR LEU THR LYS ILE LEU HIS VAL PHE HIS GLY SEQRES 10 A 460 LEU LEU PRO GLY PHE LEU VAL LYS MET SER GLY ASP LEU SEQRES 11 A 460 LEU GLU LEU ALA LEU LYS LEU PRO HIS VAL ASP TYR ILE SEQRES 12 A 460 GLU GLU ASP SER SER VAL PHE ALA GLN SER ILE PRO TRP SEQRES 13 A 460 ASN LEU GLU ARG ILE THR PRO PRO ARG TYR SER ALA ASP SEQRES 14 A 460 GLU TYR GLN PRO PRO ASP GLY GLY SER LEU VAL GLU VAL SEQRES 15 A 460 TYR LEU LEU ASP THR SER ILE GLN SER ASP HIS ARG GLU SEQRES 16 A 460 ILE GLU GLY ARG VAL MET VAL THR ASP PHE GLU ASN VAL SEQRES 17 A 460 PRO GLU GLU ASP GLY THR ARG PHE HIS ARG GLN ALA SER SEQRES 18 A 460 LYS CYS ASP SER HIS GLY THR HIS LEU ALA GLY VAL VAL SEQRES 19 A 460 SER GLY ARG ASP ALA GLY VAL ALA LYS GLY ALA SER MET SEQRES 20 A 460 ARG SER LEU ARG VAL LEU ASN CYS GLN GLY LYS GLY THR SEQRES 21 A 460 VAL SER GLY THR LEU ILE GLY LEU GLU PHE ILE ARG LYS SEQRES 22 A 460 SER GLN LEU VAL GLN PRO VAL GLY PRO LEU VAL VAL LEU SEQRES 23 A 460 LEU PRO LEU ALA GLY GLY TYR SER ARG VAL LEU ASN ALA SEQRES 24 A 460 ALA CYS GLN ARG LEU ALA ARG ALA GLY VAL VAL LEU VAL SEQRES 25 A 460 THR ALA ALA GLY ASN PHE ARG ASP ASP ALA CYS LEU TYR SEQRES 26 A 460 SER PRO ALA SER ALA PRO GLU VAL ILE THR VAL GLY ALA SEQRES 27 A 460 THR ASN ALA GLN ASP GLN PRO VAL THR LEU GLY THR LEU SEQRES 28 A 460 GLY THR ASN PHE GLY ARG CYS VAL ASP LEU PHE ALA PRO SEQRES 29 A 460 GLY GLU ASP ILE ILE GLY ALA SER SER ASP CYS SER THR SEQRES 30 A 460 CYS PHE VAL SER GLN SER GLY THR SER GLN ALA ALA ALA SEQRES 31 A 460 HIS VAL ALA GLY ILE ALA ALA MET MET LEU SER ALA GLU SEQRES 32 A 460 PRO GLU LEU THR LEU ALA GLU LEU ARG GLN ARG LEU ILE SEQRES 33 A 460 HIS PHE SER ALA LYS ASP VAL ILE ASN GLU ALA TRP PHE SEQRES 34 A 460 PRO GLU ASP GLN ARG VAL LEU THR PRO ASN LEU VAL ALA SEQRES 35 A 460 ALA LEU PRO PRO SER THR HIS GLY ALA GLY ASN SER HIS SEQRES 36 A 460 HIS HIS HIS HIS HIS SEQRES 1 Y 15 ACE THR VAL PHE THR SER TRP GLU GLU TYR LEU ASP TRP SEQRES 2 Y 15 VAL NH2 SEQRES 1 Z 11 ACE TRP ASN LEU VAL HRG ILE GLY LEU LEU ARG HET ACE Y 0 3 HET NH2 Y 14 1 HET ACE Z 0 3 HET HRG Z 5 12 HET CA A 501 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM HRG L-HOMOARGININE HETNAM CA CALCIUM ION FORMUL 2 ACE 2(C2 H4 O) FORMUL 2 NH2 H2 N FORMUL 3 HRG C7 H16 N4 O2 FORMUL 4 CA CA 2+ FORMUL 5 HOH *213(H2 O) HELIX 1 AA1 LYS A 69 PRO A 71 5 3 HELIX 2 AA2 HIS A 87 ARG A 105 1 19 HELIX 3 AA3 SER A 127 ASP A 129 5 3 HELIX 4 AA4 LEU A 130 LYS A 136 1 7 HELIX 5 AA5 ASP A 224 GLY A 236 1 13 HELIX 6 AA6 VAL A 261 GLN A 278 1 18 HELIX 7 AA7 SER A 294 ALA A 307 1 14 HELIX 8 AA8 ASP A 321 CYS A 323 5 3 HELIX 9 AA9 GLY A 384 GLU A 403 1 20 HELIX 10 AB1 THR A 407 SER A 419 1 13 HELIX 11 AB2 ASN A 425 PHE A 429 5 5 HELIX 12 AB3 PRO A 430 ARG A 434 5 5 HELIX 13 AB4 SER Y 5 VAL Y 13 1 9 HELIX 14 AB5 TRP Z 1 ILE Z 6 1 6 SHEET 1 AA1 3 THR A 63 HIS A 65 0 SHEET 2 AA1 3 VAL A 140 ALA A 151 1 O GLU A 145 N HIS A 65 SHEET 3 AA1 3 LYS A 258 THR A 260 -1 O GLY A 259 N VAL A 149 SHEET 1 AA2 6 LYS A 110 PHE A 115 0 SHEET 2 AA2 6 GLY A 121 LYS A 125 -1 O LEU A 123 N HIS A 113 SHEET 3 AA2 6 ARG A 73 LEU A 82 -1 N VAL A 80 O PHE A 122 SHEET 4 AA2 6 VAL A 140 ALA A 151 -1 O GLU A 144 N VAL A 79 SHEET 5 AA2 6 LEU A 289 GLY A 292 -1 O ALA A 290 N PHE A 150 SHEET 6 AA2 6 TYR A 325 SER A 326 -1 O SER A 326 N GLY A 291 SHEET 1 AA3 7 VAL A 200 GLU A 206 0 SHEET 2 AA3 7 SER A 246 ARG A 251 1 O MET A 247 N MET A 201 SHEET 3 AA3 7 GLU A 181 ASP A 186 1 N LEU A 184 O LEU A 250 SHEET 4 AA3 7 LEU A 283 LEU A 287 1 O LEU A 286 N TYR A 183 SHEET 5 AA3 7 VAL A 310 ALA A 314 1 O VAL A 310 N VAL A 285 SHEET 6 AA3 7 ILE A 334 THR A 339 1 O ILE A 334 N THR A 313 SHEET 7 AA3 7 LEU A 361 PRO A 364 1 O LEU A 361 N GLY A 337 SHEET 1 AA4 2 THR A 347 LEU A 348 0 SHEET 2 AA4 2 LEU A 351 GLY A 352 -1 O LEU A 351 N LEU A 348 SHEET 1 AA5 2 ILE A 368 ALA A 371 0 SHEET 2 AA5 2 PHE A 379 GLN A 382 -1 O GLN A 382 N ILE A 368 SHEET 1 AA6 2 ALA A 420 LYS A 421 0 SHEET 2 AA6 2 LEU A 440 VAL A 441 -1 O VAL A 441 N ALA A 420 SSBOND 1 CYS A 223 CYS A 255 1555 1555 2.04 SSBOND 2 CYS A 323 CYS A 358 1555 1555 2.06 SSBOND 3 CYS A 375 CYS A 378 1555 1555 2.03 LINK C ACE Y 0 N THR Y 1 1555 1555 1.34 LINK C VAL Y 13 N NH2 Y 14 1555 1555 1.28 LINK C ACE Z 0 N TRP Z 1 1555 1555 1.35 LINK C VAL Z 4 N HRG Z 5 1555 1555 1.33 LINK C HRG Z 5 N ILE Z 6 1555 1555 1.34 LINK O PRO A 331 CA CA A 501 1555 1555 2.34 LINK O VAL A 333 CA CA A 501 1555 1555 2.33 LINK OD1 ASP A 360 CA CA A 501 1555 1555 2.89 LINK OD2 ASP A 360 CA CA A 501 1555 1555 2.35 LINK CA CA A 501 O HOH A 651 1555 1555 2.53 LINK CA CA A 501 O HOH A 750 1555 1555 2.48 LINK CA CA A 501 O HOH A 753 1555 1555 2.66 CISPEP 1 SER A 326 PRO A 327 0 -0.86 SITE 1 AC1 6 PRO A 331 VAL A 333 ASP A 360 HOH A 651 SITE 2 AC1 6 HOH A 750 HOH A 753 CRYST1 70.387 70.387 156.983 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 0.014207 0.008203 0.000000 0.00000 SCALE2 0.000000 0.016405 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006370 0.00000