HEADER HYDROLASE/INHIBITOR 19-JAN-23 8FVL 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: YBX-YC3-VAL-PRO-THR-THR-PHE-MAA-CYS-MN1 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 2 30-APR-25 8FVL 1 JRNL REVDAT 1 16-OCT-24 8FVL 0 JRNL AUTH P.GROSCHE,A.N.FLYER,R.GATTLEN,M.XU,A.A.GOLOSOV,V.VERA, JRNL AUTH 2 S.PICKETT,M.E.BROUSSEAU,R.CHOPRA,K.B.CLAIRMONT,A.KOCH,E.LIU, JRNL AUTH 3 P.REID,L.PERRY,L.YANG,Q.YANG,L.G.MONOVICH JRNL TITL DISCOVERY OF TRUNCATED CYCLIC PEPTIDES TARGETING AN JRNL TITL 2 INDUCED-FIT POCKET ON PCSK9. JRNL REF CHEMMEDCHEM V. 19 00208 2024 JRNL REFN ESSN 1860-7187 JRNL PMID 39437016 JRNL DOI 10.1002/CMDC.202400208 REMARK 2 REMARK 2 RESOLUTION. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 48744 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2465 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 44.9130 - 5.1369 0.99 2754 149 0.2044 0.1994 REMARK 3 2 5.1369 - 4.0781 1.00 2641 139 0.1607 0.1548 REMARK 3 3 4.0781 - 3.5629 1.00 2608 135 0.1711 0.2206 REMARK 3 4 3.5629 - 3.2372 1.00 2619 114 0.1808 0.2008 REMARK 3 5 3.2372 - 3.0053 1.00 2567 142 0.1925 0.2086 REMARK 3 6 3.0053 - 2.8281 1.00 2579 134 0.1898 0.2388 REMARK 3 7 2.8281 - 2.6865 1.00 2568 136 0.1958 0.2511 REMARK 3 8 2.6865 - 2.5696 1.00 2557 125 0.2037 0.2236 REMARK 3 9 2.5696 - 2.4706 1.00 2571 139 0.2000 0.2254 REMARK 3 10 2.4706 - 2.3854 1.00 2548 136 0.2042 0.2433 REMARK 3 11 2.3854 - 2.3108 1.00 2534 139 0.2007 0.2607 REMARK 3 12 2.3108 - 2.2448 1.00 2519 156 0.2030 0.2589 REMARK 3 13 2.2448 - 2.1857 1.00 2551 132 0.2141 0.2236 REMARK 3 14 2.1857 - 2.1323 1.00 2557 128 0.2077 0.2035 REMARK 3 15 2.1323 - 2.0839 1.00 2520 143 0.2265 0.2642 REMARK 3 16 2.0839 - 2.0395 1.00 2509 149 0.2327 0.2544 REMARK 3 17 2.0395 - 1.9987 1.00 2564 125 0.2362 0.2744 REMARK 3 18 1.9987 - 1.9610 1.00 2513 144 0.2418 0.2650 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.200 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 : 0.011 4473 REMARK 3 ANGLE : 1.509 6054 REMARK 3 CHIRALITY : 0.092 695 REMARK 3 PLANARITY : 0.009 785 REMARK 3 DIHEDRAL : 15.154 1615 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 8FVL 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_1000271279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-13 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 : 48832 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.961 REMARK 200 RESOLUTION RANGE LOW (A) : 149.679 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.00500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 (%): 43.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 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 74.83950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.33750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.56600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.33750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 74.83950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.56600 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: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 YBX-YC3-VAL-PRO-THR-THR-PHE-MAA-CYS-MN1 INHIBITOR IS CYCLIC REMARK 400 PEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: YBX-YC3-VAL-PRO-THR-THR-PHE-MAA-CYS-MN1 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 IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 711 O HOH B 886 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 3554 2.15 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 -5.61 73.40 REMARK 500 ASP B 186 -158.08 -161.76 REMARK 500 GLU B 197 125.63 -33.11 REMARK 500 ALA B 242 71.59 -113.15 REMARK 500 VAL B 280 -146.84 -126.81 REMARK 500 GLU B 332 -6.08 80.71 REMARK 500 GLN B 503 112.28 -168.52 REMARK 500 ASP B 651 -115.34 56.65 REMARK 500 MAA L 8 52.60 -119.82 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 -148.96 REMARK 500 LYS B 494 ARG B 495 -149.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FVL A 1 152 UNP Q8NBP7 PCSK9_HUMAN 1 152 DBREF 8FVL B 153 692 UNP Q8NBP7 PCSK9_HUMAN 153 692 DBREF 8FVL L 1 10 PDB 8FVL 8FVL 1 10 SEQADV 8FVL ILE B 474 UNP Q8NBP7 VAL 474 VARIANT SEQADV 8FVL 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 10 YBX YC3 VAL PRO THR THR PHE MAA CYS MN1 HET YBX L 1 6 HET YC3 L 2 19 HET MAA L 8 6 HET MN1 L 10 9 HETNAM YBX (ETHYLSULFANYL)ACETIC ACID HETNAM YC3 3-[2-(SULFANYLMETHYL)PHENYL]-L-PHENYLALANINE HETNAM MAA N-METHYL-L-ALANINE HETNAM MN1 4-CARBOXYPIPERIDINE FORMUL 3 YBX C4 H8 O2 S FORMUL 3 YC3 C16 H17 N O2 S FORMUL 3 MAA C4 H9 N O2 FORMUL 3 MN1 C6 H11 N O2 FORMUL 4 HOH *305(H2 O) HELIX 1 AA1 LYS A 69 PRO A 71 5 3 HELIX 2 AA2 HIS A 87 ARG A 104 1 18 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 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 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 LYS A 125 N LYS A 110 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 LEU B 311 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 CYS B 509 N ALA B 475 SHEET 3 AA8 3 ARG B 495 GLN B 503 -1 N ARG B 499 O ARG B 510 SHEET 1 AA9 3 ASN B 533 ALA B 539 0 SHEET 2 AA9 3 SER B 595 HIS B 602 -1 O CYS B 600 N SER B 535 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 CYS B 678 N LYS B 609 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 2.07 SSBOND 2 CYS B 323 CYS B 358 1555 1555 2.09 SSBOND 3 CYS B 375 CYS B 378 1555 1555 2.04 SSBOND 4 CYS B 457 CYS B 527 1555 1555 2.05 SSBOND 5 CYS B 477 CYS B 526 1555 1555 2.04 SSBOND 6 CYS B 486 CYS B 509 1555 1555 2.05 SSBOND 7 CYS B 534 CYS B 601 1555 1555 2.05 SSBOND 8 CYS B 552 CYS B 600 1555 1555 2.03 SSBOND 9 CYS B 562 CYS B 588 1555 1555 2.03 SSBOND 10 CYS B 608 CYS B 679 1555 1555 2.04 SSBOND 11 CYS B 626 CYS B 678 1555 1555 2.04 SSBOND 12 CYS B 635 CYS B 654 1555 1555 2.03 SSBOND 13 YC3 L 2 CYS L 9 1555 1555 2.07 LINK C5 YBX L 1 N YC3 L 2 1555 1555 1.32 LINK C YC3 L 2 N VAL L 3 1555 1555 1.34 LINK C PHE L 7 N MAA L 8 1555 1555 1.36 LINK C MAA L 8 N CYS L 9 1555 1555 1.32 LINK C CYS L 9 N MN1 L 10 1555 1555 1.35 CISPEP 1 SER B 326 PRO B 327 0 -0.99 CISPEP 2 PHE L 7 MAA L 8 0 0.34 CRYST1 149.679 63.132 70.675 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 0.006681 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014149 0.00000 CONECT 1193 1416 CONECT 1416 1193 CONECT 1907 2155 CONECT 2155 1907 CONECT 2273 2292 CONECT 2292 2273 CONECT 2882 3403 CONECT 3032 3397 CONECT 3098 3272 CONECT 3272 3098 CONECT 3397 3032 CONECT 3403 2882 CONECT 3454 3805 CONECT 3553 3799 CONECT 3605 3712 CONECT 3712 3605 CONECT 3799 3553 CONECT 3805 3454 CONECT 3854 4261 CONECT 3976 4255 CONECT 4044 4163 CONECT 4163 4044 CONECT 4255 3976 CONECT 4261 3854 CONECT 4280 4281 CONECT 4281 4280 4282 4303 CONECT 4282 4281 4283 CONECT 4283 4282 4284 CONECT 4284 4283 4285 CONECT 4285 4284 CONECT 4286 4287 4290 4305 CONECT 4287 4286 4288 4303 CONECT 4288 4287 4289 CONECT 4289 4288 4291 4295 CONECT 4290 4286 CONECT 4291 4289 4292 CONECT 4292 4291 4293 4296 CONECT 4293 4292 4294 CONECT 4294 4293 4295 CONECT 4295 4289 4294 CONECT 4296 4292 4297 4301 CONECT 4297 4296 4298 CONECT 4298 4297 4299 CONECT 4299 4298 4300 CONECT 4300 4299 4301 CONECT 4301 4296 4300 4302 CONECT 4302 4301 4304 CONECT 4303 4281 4287 CONECT 4304 4302 4355 CONECT 4305 4286 CONECT 4335 4344 CONECT 4344 4335 4345 4346 CONECT 4345 4344 CONECT 4346 4344 4347 4348 CONECT 4347 4346 CONECT 4348 4346 4349 4350 CONECT 4349 4348 CONECT 4350 4348 CONECT 4352 4356 CONECT 4355 4304 CONECT 4356 4352 4357 4364 CONECT 4357 4356 4358 CONECT 4358 4357 4359 CONECT 4359 4358 4360 4363 CONECT 4360 4359 4361 4362 CONECT 4361 4360 CONECT 4362 4360 CONECT 4363 4359 4364 CONECT 4364 4356 4363 MASTER 418 0 4 13 39 0 0 6 4667 3 69 55 END