HEADER HYDROLASE/INHIBITOR 19-JAN-23 8FVP TITLE PCSK9 IN COMPLEX WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PRODOMAIN RESIDUES 1-152; 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 MOL_ID: 2; COMPND 10 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1,NARC-1,PROPROTEIN COMPND 13 CONVERTASE 9,PC9,SUBTILISIN/KEXIN-LIKE PROTEASE PC9; COMPND 14 EC: 3.4.21.-; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: PPI-YD5-NLE-7T2-SER-7T2-DPP-GLY-NH2 INHIBITOR; COMPND 18 CHAIN: L; COMPND 19 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: PCSK9, NARC1, PSEC0052; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS COMPLEX, INHIBITOR, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.XU,R.CHOPRA REVDAT 1 16-OCT-24 8FVP 0 JRNL AUTH M.XU,R.CHOPRA JRNL TITL PCSK9 IN COMPLEX WITH CYCLIC PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21182 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.9620 - 5.2014 1.00 2680 133 0.1748 0.1767 REMARK 3 2 5.2014 - 4.1293 1.00 2552 123 0.1471 0.1945 REMARK 3 3 4.1293 - 3.6075 1.00 2487 153 0.1671 0.1945 REMARK 3 4 3.6075 - 3.2778 1.00 2515 112 0.1833 0.2111 REMARK 3 5 3.2778 - 3.0429 1.00 2486 138 0.1920 0.2567 REMARK 3 6 3.0429 - 2.8635 1.00 2456 131 0.1991 0.2150 REMARK 3 7 2.8635 - 2.7201 1.00 2465 134 0.2129 0.2804 REMARK 3 8 2.7201 - 2.6020 1.00 2483 134 0.2308 0.3383 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 4449 REMARK 3 ANGLE : 1.534 6019 REMARK 3 CHIRALITY : 0.090 689 REMARK 3 PLANARITY : 0.008 783 REMARK 3 DIHEDRAL : 15.265 1600 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8FVP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21242 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.602 REMARK 200 RESOLUTION RANGE LOW (A) : 150.112 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: FFT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.0% PEG-6000, 0.1M TRIS PH8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 31.51650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.05600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.20350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.05600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.51650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.20350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, L 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 PPI-YD5-NLE-7T2-SER-7T2-DPP-GLY-NH2 INHIBITOR IS CYCLIC PEPTIDE, REMARK 400 A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PPI-YD5-NLE-7T2-SER-7T2-DPP-GLY-NH2 INHIBITOR REMARK 400 CHAIN: L 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 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 ALA B 168 REMARK 465 ASP B 169 REMARK 465 GLU B 170 REMARK 465 TYR B 171 REMARK 465 GLN B 172 REMARK 465 PRO B 173 REMARK 465 PRO B 174 REMARK 465 ASP B 175 REMARK 465 GLY B 213 REMARK 465 THR B 214 REMARK 465 ARG B 215 REMARK 465 PHE B 216 REMARK 465 HIS B 217 REMARK 465 ARG B 218 REMARK 465 GLN B 219 REMARK 465 GLY B 450 REMARK 465 ALA B 451 REMARK 465 GLU B 543 REMARK 465 ALA B 544 REMARK 465 SER B 545 REMARK 465 MET B 546 REMARK 465 GLN B 554 REMARK 465 GLN B 555 REMARK 465 GLY B 556 REMARK 465 GLY B 572 REMARK 465 THR B 573 REMARK 465 HIS B 574 REMARK 465 LYS B 575 REMARK 465 PRO B 576 REMARK 465 PRO B 577 REMARK 465 VAL B 578 REMARK 465 LEU B 579 REMARK 465 ARG B 580 REMARK 465 PRO B 581 REMARK 465 ARG B 582 REMARK 465 GLY B 583 REMARK 465 GLN B 584 REMARK 465 ALA B 617 REMARK 465 PRO B 618 REMARK 465 GLY B 640 REMARK 465 THR B 641 REMARK 465 ASP B 660 REMARK 465 VAL B 661 REMARK 465 SER B 662 REMARK 465 THR B 663 REMARK 465 THR B 664 REMARK 465 GLY B 665 REMARK 465 SER B 666 REMARK 465 THR B 667 REMARK 465 SER B 668 REMARK 465 GLU B 669 REMARK 465 GLU B 670 REMARK 465 ARG B 682 REMARK 465 HIS B 683 REMARK 465 LEU B 684 REMARK 465 ALA B 685 REMARK 465 GLN B 686 REMARK 465 ALA B 687 REMARK 465 SER B 688 REMARK 465 GLN B 689 REMARK 465 GLU B 690 REMARK 465 LEU B 691 REMARK 465 GLN B 692 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 NH1 ARG B 165 OE2 GLU B 612 4555 2.18 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 VAL B 423 CB VAL B 423 CG1 -0.145 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 HIS A 139 -4.86 72.82 REMARK 500 ASP B 186 -157.20 -162.61 REMARK 500 GLU B 197 125.71 -34.02 REMARK 500 ALA B 242 72.69 -113.49 REMARK 500 VAL B 280 -146.82 -126.21 REMARK 500 GLU B 332 -5.49 81.01 REMARK 500 GLN B 503 111.72 -168.47 REMARK 500 ASP B 651 -116.01 57.01 REMARK 500 7T2 L 4 78.11 58.43 REMARK 500 DPP L 7 17.62 53.64 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 GLY B 244 ALA B 245 -148.49 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 B 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL B 333 O REMARK 620 2 CYS B 358 O 125.6 REMARK 620 3 ASP B 360 OD2 60.3 77.3 REMARK 620 N 1 2 DBREF 8FVP A 1 152 UNP Q8NBP7 PCSK9_HUMAN 1 152 DBREF 8FVP B 153 692 UNP Q8NBP7 PCSK9_HUMAN 153 692 DBREF 8FVP L 1 9 PDB 8FVP 8FVP 1 9 SEQADV 8FVP ILE B 474 UNP Q8NBP7 VAL 474 VARIANT SEQADV 8FVP GLU B 670 UNP Q8NBP7 GLY 670 VARIANT SEQRES 1 A 152 MET GLY THR VAL SER SER ARG ARG SER TRP TRP PRO LEU SEQRES 2 A 152 PRO LEU LEU LEU LEU LEU LEU LEU LEU LEU GLY PRO ALA SEQRES 3 A 152 GLY ALA ARG ALA GLN GLU ASP GLU ASP GLY ASP TYR GLU SEQRES 4 A 152 GLU LEU VAL LEU ALA LEU ARG SER GLU GLU ASP GLY LEU SEQRES 5 A 152 ALA GLU ALA PRO GLU HIS GLY THR THR ALA THR PHE HIS SEQRES 6 A 152 ARG CYS ALA LYS ASP PRO TRP ARG LEU PRO GLY THR TYR SEQRES 7 A 152 VAL VAL VAL LEU LYS GLU GLU THR HIS LEU SER GLN SER SEQRES 8 A 152 GLU ARG THR ALA ARG ARG LEU GLN ALA GLN ALA ALA ARG SEQRES 9 A 152 ARG GLY TYR LEU THR LYS ILE LEU HIS VAL PHE HIS GLY SEQRES 10 A 152 LEU LEU PRO GLY PHE LEU VAL LYS MET SER GLY ASP LEU SEQRES 11 A 152 LEU GLU LEU ALA LEU LYS LEU PRO HIS VAL ASP TYR ILE SEQRES 12 A 152 GLU GLU ASP SER SER VAL PHE ALA GLN SEQRES 1 B 540 SER ILE PRO TRP ASN LEU GLU ARG ILE THR PRO PRO ARG SEQRES 2 B 540 TYR ARG ALA ASP GLU TYR GLN PRO PRO ASP GLY GLY SER SEQRES 3 B 540 LEU VAL GLU VAL TYR LEU LEU ASP THR SER ILE GLN SER SEQRES 4 B 540 ASP HIS ARG GLU ILE GLU GLY ARG VAL MET VAL THR ASP SEQRES 5 B 540 PHE GLU ASN VAL PRO GLU GLU ASP GLY THR ARG PHE HIS SEQRES 6 B 540 ARG GLN ALA SER LYS CYS ASP SER HIS GLY THR HIS LEU SEQRES 7 B 540 ALA GLY VAL VAL SER GLY ARG ASP ALA GLY VAL ALA LYS SEQRES 8 B 540 GLY ALA SER MET ARG SER LEU ARG VAL LEU ASN CYS GLN SEQRES 9 B 540 GLY LYS GLY THR VAL SER GLY THR LEU ILE GLY LEU GLU SEQRES 10 B 540 PHE ILE ARG LYS SER GLN LEU VAL GLN PRO VAL GLY PRO SEQRES 11 B 540 LEU VAL VAL LEU LEU PRO LEU ALA GLY GLY TYR SER ARG SEQRES 12 B 540 VAL LEU ASN ALA ALA CYS GLN ARG LEU ALA ARG ALA GLY SEQRES 13 B 540 VAL VAL LEU VAL THR ALA ALA GLY ASN PHE ARG ASP ASP SEQRES 14 B 540 ALA CYS LEU TYR SER PRO ALA SER ALA PRO GLU VAL ILE SEQRES 15 B 540 THR VAL GLY ALA THR ASN ALA GLN ASP GLN PRO VAL THR SEQRES 16 B 540 LEU GLY THR LEU GLY THR ASN PHE GLY ARG CYS VAL ASP SEQRES 17 B 540 LEU PHE ALA PRO GLY GLU ASP ILE ILE GLY ALA SER SER SEQRES 18 B 540 ASP CYS SER THR CYS PHE VAL SER GLN SER GLY THR SER SEQRES 19 B 540 GLN ALA ALA ALA HIS VAL ALA GLY ILE ALA ALA MET MET SEQRES 20 B 540 LEU SER ALA GLU PRO GLU LEU THR LEU ALA GLU LEU ARG SEQRES 21 B 540 GLN ARG LEU ILE HIS PHE SER ALA LYS ASP VAL ILE ASN SEQRES 22 B 540 GLU ALA TRP PHE PRO GLU ASP GLN ARG VAL LEU THR PRO SEQRES 23 B 540 ASN LEU VAL ALA ALA LEU PRO PRO SER THR HIS GLY ALA SEQRES 24 B 540 GLY TRP GLN LEU PHE CYS ARG THR VAL TRP SER ALA HIS SEQRES 25 B 540 SER GLY PRO THR ARG MET ALA THR ALA ILE ALA ARG CYS SEQRES 26 B 540 ALA PRO ASP GLU GLU LEU LEU SER CYS SER SER PHE SER SEQRES 27 B 540 ARG SER GLY LYS ARG ARG GLY GLU ARG MET GLU ALA GLN SEQRES 28 B 540 GLY GLY LYS LEU VAL CYS ARG ALA HIS ASN ALA PHE GLY SEQRES 29 B 540 GLY GLU GLY VAL TYR ALA ILE ALA ARG CYS CYS LEU LEU SEQRES 30 B 540 PRO GLN ALA ASN CYS SER VAL HIS THR ALA PRO PRO ALA SEQRES 31 B 540 GLU ALA SER MET GLY THR ARG VAL HIS CYS HIS GLN GLN SEQRES 32 B 540 GLY HIS VAL LEU THR GLY CYS SER SER HIS TRP GLU VAL SEQRES 33 B 540 GLU ASP LEU GLY THR HIS LYS PRO PRO VAL LEU ARG PRO SEQRES 34 B 540 ARG GLY GLN PRO ASN GLN CYS VAL GLY HIS ARG GLU ALA SEQRES 35 B 540 SER ILE HIS ALA SER CYS CYS HIS ALA PRO GLY LEU GLU SEQRES 36 B 540 CYS LYS VAL LYS GLU HIS GLY ILE PRO ALA PRO GLN GLU SEQRES 37 B 540 GLN VAL THR VAL ALA CYS GLU GLU GLY TRP THR LEU THR SEQRES 38 B 540 GLY CYS SER ALA LEU PRO GLY THR SER HIS VAL LEU GLY SEQRES 39 B 540 ALA TYR ALA VAL ASP ASN THR CYS VAL VAL ARG SER ARG SEQRES 40 B 540 ASP VAL SER THR THR GLY SER THR SER GLU GLU ALA VAL SEQRES 41 B 540 THR ALA VAL ALA ILE CYS CYS ARG SER ARG HIS LEU ALA SEQRES 42 B 540 GLN ALA SER GLN GLU LEU GLN SEQRES 1 L 9 PPI YD5 NLE 7T2 SER 7T2 DPP GLY NH2 HET PPI L 1 4 HET YD5 L 2 9 HET NLE L 3 8 HET 7T2 L 4 13 HET 7T2 L 6 13 HET DPP L 7 6 HET NH2 L 9 1 HET CA B 701 1 HETNAM PPI PROPANOIC ACID HETNAM YD5 N-(2-CARBOXYETHYL)-L-ALANINE HETNAM NLE NORLEUCINE HETNAM 7T2 (2S)-3-(4-CHLOROPHENYL)-2-(METHYLAMINO)PROPANOIC ACID HETNAM DPP DIAMINOPROPANOIC ACID HETNAM NH2 AMINO GROUP HETNAM CA CALCIUM ION FORMUL 3 PPI C3 H6 O2 FORMUL 3 YD5 C6 H11 N O4 FORMUL 3 NLE C6 H13 N O2 FORMUL 3 7T2 2(C10 H12 CL N O2) FORMUL 3 DPP C3 H8 N2 O2 FORMUL 3 NH2 H2 N FORMUL 4 CA CA 2+ FORMUL 5 HOH *82(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 PRO B 155 ILE B 161 1 7 HELIX 6 AA6 ASP B 224 GLY B 236 1 13 HELIX 7 AA7 VAL B 261 GLN B 278 1 18 HELIX 8 AA8 SER B 294 ALA B 307 1 14 HELIX 9 AA9 ASP B 321 CYS B 323 5 3 HELIX 10 AB1 GLY B 384 GLU B 403 1 20 HELIX 11 AB2 THR B 407 PHE B 418 1 12 HELIX 12 AB3 ASN B 425 PHE B 429 5 5 HELIX 13 AB4 PRO B 430 ARG B 434 5 5 HELIX 14 AB5 NLE L 3 GLY L 8 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 ILE A 143 N THR A 63 SHEET 3 AA1 3 LYS B 258 THR B 260 -1 O GLY B 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 B 289 GLY B 292 -1 O ALA B 290 N PHE A 150 SHEET 6 AA2 6 TYR B 325 SER B 326 -1 O SER B 326 N GLY B 291 SHEET 1 AA3 7 VAL B 200 GLU B 206 0 SHEET 2 AA3 7 SER B 246 ARG B 251 1 O MET B 247 N MET B 201 SHEET 3 AA3 7 GLU B 181 ASP B 186 1 N LEU B 184 O ARG B 248 SHEET 4 AA3 7 LEU B 283 LEU B 287 1 O VAL B 284 N TYR B 183 SHEET 5 AA3 7 VAL B 310 ALA B 314 1 O VAL B 310 N VAL B 285 SHEET 6 AA3 7 ILE B 334 THR B 339 1 O ILE B 334 N THR B 313 SHEET 7 AA3 7 LEU B 361 PRO B 364 1 O LEU B 361 N GLY B 337 SHEET 1 AA4 2 THR B 347 LEU B 348 0 SHEET 2 AA4 2 LEU B 351 GLY B 352 -1 O LEU B 351 N LEU B 348 SHEET 1 AA5 2 ILE B 368 ALA B 371 0 SHEET 2 AA5 2 PHE B 379 GLN B 382 -1 O GLN B 382 N ILE B 368 SHEET 1 AA6 2 ALA B 420 LYS B 421 0 SHEET 2 AA6 2 LEU B 440 VAL B 441 -1 O VAL B 441 N ALA B 420 SHEET 1 AA7 3 PHE B 456 TRP B 461 0 SHEET 2 AA7 3 TYR B 521 LEU B 528 -1 O ALA B 524 N VAL B 460 SHEET 3 AA7 3 GLU B 482 PHE B 489 -1 N GLU B 482 O CYS B 527 SHEET 1 AA8 3 THR B 472 ALA B 475 0 SHEET 2 AA8 3 LYS B 506 ASN B 513 -1 O ALA B 511 N ALA B 473 SHEET 3 AA8 3 ARG B 495 GLN B 503 -1 N ARG B 496 O HIS B 512 SHEET 1 AA9 3 ASN B 533 ALA B 539 0 SHEET 2 AA9 3 SER B 595 HIS B 602 -1 O HIS B 602 N ASN B 533 SHEET 3 AA9 3 VAL B 558 HIS B 565 -1 N HIS B 565 O SER B 595 SHEET 1 AB1 2 THR B 548 HIS B 551 0 SHEET 2 AB1 2 GLN B 587 GLY B 590 -1 O GLY B 590 N THR B 548 SHEET 1 AB2 3 GLU B 607 ILE B 615 0 SHEET 2 AB2 3 VAL B 672 ARG B 680 -1 O ARG B 680 N GLU B 607 SHEET 3 AB2 3 THR B 631 ALA B 637 -1 N THR B 631 O CYS B 679 SHEET 1 AB3 3 GLN B 621 ALA B 625 0 SHEET 2 AB3 3 THR B 653 SER B 658 -1 O CYS B 654 N VAL B 624 SHEET 3 AB3 3 VAL B 644 VAL B 650 -1 N VAL B 650 O THR B 653 SSBOND 1 CYS B 223 CYS B 255 1555 1555 2.06 SSBOND 2 CYS B 323 CYS B 358 1555 1555 2.10 SSBOND 3 CYS B 375 CYS B 378 1555 1555 2.07 SSBOND 4 CYS B 457 CYS B 527 1555 1555 2.01 SSBOND 5 CYS B 477 CYS B 526 1555 1555 2.05 SSBOND 6 CYS B 486 CYS B 509 1555 1555 2.04 SSBOND 7 CYS B 534 CYS B 601 1555 1555 2.04 SSBOND 8 CYS B 552 CYS B 600 1555 1555 2.04 SSBOND 9 CYS B 562 CYS B 588 1555 1555 2.04 SSBOND 10 CYS B 608 CYS B 679 1555 1555 2.04 SSBOND 11 CYS B 626 CYS B 678 1555 1555 2.05 SSBOND 12 CYS B 635 CYS B 654 1555 1555 2.03 LINK C1 PPI L 1 N YD5 L 2 1555 1555 1.36 LINK C YD5 L 2 N NLE L 3 1555 1555 1.34 LINK C4 YD5 L 2 NG DPP L 7 1555 1555 1.34 LINK C NLE L 3 N 7T2 L 4 1555 1555 1.36 LINK C 7T2 L 4 N SER L 5 1555 1555 1.34 LINK C SER L 5 N 7T2 L 6 1555 1555 1.36 LINK C 7T2 L 6 N DPP L 7 1555 1555 1.34 LINK C DPP L 7 N GLY L 8 1555 1555 1.34 LINK C GLY L 8 N NH2 L 9 1555 1555 1.33 LINK O VAL B 333 CA CA B 701 1555 1555 3.14 LINK O CYS B 358 CA CA B 701 1555 1555 3.14 LINK OD2 ASP B 360 CA CA B 701 1555 1555 3.10 CISPEP 1 SER B 326 PRO B 327 0 -0.69 CRYST1 63.033 70.407 150.112 90.00 90.00 90.00 P 21 21 21 4 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 0.015865 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006662 0.00000