HEADER HYDROLASE/INHIBITOR 19-JUN-20 6XIE TITLE PCSK9(DELTACRD) IN COMPLEX WITH CYCLIC PEPTIDE 77 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1,NARC-1,PROPROTEIN COMPND 5 CONVERTASE 9,PC9,SUBTILISIN/KEXIN-LIKE PROTEASE PC9; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1,NARC-1,PROPROTEIN COMPND 12 CONVERTASE 9,PC9,SUBTILISIN/KEXIN-LIKE PROTEASE PC9; COMPND 13 EC: 3.4.21.-; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: PEPTIDE 77; COMPND 17 CHAIN: I; 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 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PCSK9, NARC1, PSEC0052; SOURCE 15 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 16 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-PEPTIDE COMPLEX, CYCLIC PEPTIDE, NON-NATURAL AMINO ACIDS, KEYWDS 2 HYDROLASE, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.ORTH REVDAT 5 24-APR-24 6XIE 1 COMPND SOURCE REMARK DBREF REVDAT 5 2 1 SEQRES HET HETNAM HETSYN REVDAT 5 3 1 FORMUL SHEET LINK SITE REVDAT 5 4 1 ATOM REVDAT 4 15-NOV-23 6XIE 1 LINK REVDAT 3 18-OCT-23 6XIE 1 REMARK REVDAT 2 02-DEC-20 6XIE 1 JRNL REVDAT 1 18-NOV-20 6XIE 0 JRNL AUTH C.ALLEYNE,R.P.AMIN,B.BHATT,E.BIANCHI,J.C.BLAIN,N.BOYER, JRNL AUTH 2 D.BRANCA,M.W.EMBREY,S.N.HA,K.JETTE,D.G.JOHNS,A.D.KEREKES, JRNL AUTH 3 K.A.KOEPLINGER,D.LAPLACA,N.LI,B.MURPHY,P.ORTH,A.RICARDO, JRNL AUTH 4 S.SALOWE,K.SEYB,A.SHAHRIPOUR,J.R.STRINGER,Y.SUN,R.TRACY, JRNL AUTH 5 C.WU,Y.XIONG,H.YOUM,H.J.ZOKIAN,T.J.TUCKER JRNL TITL SERIES OF NOVEL AND HIGHLY POTENT CYCLIC PEPTIDE PCSK9 JRNL TITL 2 INHIBITORS DERIVED FROM AN MRNA DISPLAY SCREEN AND OPTIMIZED JRNL TITL 3 VIA STRUCTURE-BASED DESIGN. JRNL REF J.MED.CHEM. V. 63 13796 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 33170686 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01084 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 (6-FEB-2020) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 80552 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4026 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.48 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 19.37 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1612 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2278 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1536 REMARK 3 BIN R VALUE (WORKING SET) : 0.2278 REMARK 3 BIN FREE R VALUE : 0.2280 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.71 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2857 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 344 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04750 REMARK 3 B22 (A**2) : 0.04750 REMARK 3 B33 (A**2) : -0.09510 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.220 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.067 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.068 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.064 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.065 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2927 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3980 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 980 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 500 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2926 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 382 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2937 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.94 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.54 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 13.87 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80563 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 61.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4NMX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 200MM CACL2, 100MM MES PH REMARK 280 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 55.43467 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 110.86933 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 110.86933 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 55.43467 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: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 720 LIES ON A SPECIAL POSITION. 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 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 PRO B 164 REMARK 465 ARG B 165 REMARK 465 TYR B 166 REMARK 465 ARG B 167 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 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 SER B 447 REMARK 465 THR B 448 REMARK 465 HIS B 449 REMARK 465 GLY B 450 REMARK 465 ALA B 451 REMARK 465 GLY B 452 REMARK 465 ASN B 453 REMARK 465 SER B 454 REMARK 465 HIS B 455 REMARK 465 HIS B 456 REMARK 465 HIS B 457 REMARK 465 HIS B 458 REMARK 465 HIS B 459 REMARK 465 HIS B 460 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET B 201 CG SD CE REMARK 470 GLU B 210 CG CD OE1 OE2 REMARK 470 LYS B 222 CG CD CE NZ REMARK 470 ARG B 303 CZ NH1 NH2 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 501 O HOH B 503 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 Z9J I 1 CA - C - N ANGL. DEV. = 24.8 DEGREES 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 GLU A 85 -2.05 84.69 REMARK 500 HIS A 139 -6.36 74.59 REMARK 500 ASP B 186 -157.94 -159.86 REMARK 500 ALA B 242 77.69 -115.74 REMARK 500 VAL B 280 -139.53 -127.22 REMARK 500 LEU B 351 -151.44 -106.69 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 Z9J I 1 ALA I 2 85.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 Z9J I 1 -45.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 722 DISTANCE = 6.27 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues 0A1 I 9 through REMARK 800 CYS I 2 bound to THR I 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues APD I 5 and FTR I 6 DBREF 6XIE A 31 152 UNP Q8NBP7 PCSK9_HUMAN 31 152 DBREF 6XIE B 153 452 UNP Q8NBP7 PCSK9_HUMAN 153 452 DBREF 6XIE I 1 9 PDB 6XIE 6XIE 1 9 SEQADV 6XIE ASN B 453 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE SER B 454 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE HIS B 455 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE HIS B 456 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE HIS B 457 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE HIS B 458 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE HIS B 459 UNP Q8NBP7 EXPRESSION TAG SEQADV 6XIE HIS B 460 UNP Q8NBP7 EXPRESSION TAG SEQRES 1 A 122 GLN GLU ASP GLU ASP GLY ASP TYR GLU GLU LEU VAL LEU SEQRES 2 A 122 ALA LEU ARG SER GLU GLU ASP GLY LEU ALA GLU ALA PRO SEQRES 3 A 122 GLU HIS GLY THR THR ALA THR PHE HIS ARG CYS ALA LYS SEQRES 4 A 122 ASP PRO TRP ARG LEU PRO GLY THR TYR VAL VAL VAL LEU SEQRES 5 A 122 LYS GLU GLU THR HIS LEU SER GLN SER GLU ARG THR ALA SEQRES 6 A 122 ARG ARG LEU GLN ALA GLN ALA ALA ARG ARG GLY TYR LEU SEQRES 7 A 122 THR LYS ILE LEU HIS VAL PHE HIS GLY LEU LEU PRO GLY SEQRES 8 A 122 PHE LEU VAL LYS MET SER GLY ASP LEU LEU GLU LEU ALA SEQRES 9 A 122 LEU LYS LEU PRO HIS VAL ASP TYR ILE GLU GLU ASP SER SEQRES 10 A 122 SER VAL PHE ALA GLN SEQRES 1 B 308 SER ILE PRO TRP ASN LEU GLU ARG ILE THR PRO PRO ARG SEQRES 2 B 308 TYR ARG ALA ASP GLU TYR GLN PRO PRO ASP GLY GLY SER SEQRES 3 B 308 LEU VAL GLU VAL TYR LEU LEU ASP THR SER ILE GLN SER SEQRES 4 B 308 ASP HIS ARG GLU ILE GLU GLY ARG VAL MET VAL THR ASP SEQRES 5 B 308 PHE GLU ASN VAL PRO GLU GLU ASP GLY THR ARG PHE HIS SEQRES 6 B 308 ARG GLN ALA SER LYS CYS ASP SER HIS GLY THR HIS LEU SEQRES 7 B 308 ALA GLY VAL VAL SER GLY ARG ASP ALA GLY VAL ALA LYS SEQRES 8 B 308 GLY ALA SER MET ARG SER LEU ARG VAL LEU ASN CYS GLN SEQRES 9 B 308 GLY LYS GLY THR VAL SER GLY THR LEU ILE GLY LEU GLU SEQRES 10 B 308 PHE ILE ARG LYS SER GLN LEU VAL GLN PRO VAL GLY PRO SEQRES 11 B 308 LEU VAL VAL LEU LEU PRO LEU ALA GLY GLY TYR SER ARG SEQRES 12 B 308 VAL LEU ASN ALA ALA CYS GLN ARG LEU ALA ARG ALA GLY SEQRES 13 B 308 VAL VAL LEU VAL THR ALA ALA GLY ASN PHE ARG ASP ASP SEQRES 14 B 308 ALA CYS LEU TYR SER PRO ALA SER ALA PRO GLU VAL ILE SEQRES 15 B 308 THR VAL GLY ALA THR ASN ALA GLN ASP GLN PRO VAL THR SEQRES 16 B 308 LEU GLY THR LEU GLY THR ASN PHE GLY ARG CYS VAL ASP SEQRES 17 B 308 LEU PHE ALA PRO GLY GLU ASP ILE ILE GLY ALA SER SER SEQRES 18 B 308 ASP CYS SER THR CYS PHE VAL SER GLN SER GLY THR SER SEQRES 19 B 308 GLN ALA ALA ALA HIS VAL ALA GLY ILE ALA ALA MET MET SEQRES 20 B 308 LEU SER ALA GLU PRO GLU LEU THR LEU ALA GLU LEU ARG SEQRES 21 B 308 GLN ARG LEU ILE HIS PHE SER ALA LYS ASP VAL ILE ASN SEQRES 22 B 308 GLU ALA TRP PHE PRO GLU ASP GLN ARG VAL LEU THR PRO SEQRES 23 B 308 ASN LEU VAL ALA ALA LEU PRO PRO SER THR HIS GLY ALA SEQRES 24 B 308 GLY ASN SER HIS HIS HIS HIS HIS HIS SEQRES 1 I 9 Z9J ALA DAL APD FTR GLN THR 0A1 3WX HET Z9J I 1 17 HET DAL I 3 5 HET APD I 4 12 HET FTR I 5 15 HET 0A1 I 8 13 HET 3WX I 9 8 HET GOL A 201 6 HETNAM Z9J 3-{[(3-{[(2-AMINOETHYL)SULFANYL]METHYL}PHENYL) HETNAM 2 Z9J METHYL]SULFANYL}PROPANOIC ACID HETNAM DAL D-ALANINE HETNAM APD 3-METHYLPHENYLALANINE HETNAM FTR FLUOROTRYPTOPHANE HETNAM 0A1 O-METHYL-L-TYROSINE HETNAM 3WX 2-METHYL-L-PROLINE HETNAM GOL GLYCEROL HETSYN Z9J 3-[[3-(2-AZANYLETHYLSULFANYLMETHYL) HETSYN 2 Z9J PHENYL]METHYLSULFANYL]PROPANOIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 Z9J C13 H19 N O2 S2 FORMUL 3 DAL C3 H7 N O2 FORMUL 3 APD C10 H13 N O2 FORMUL 3 FTR C11 H11 F N2 O2 FORMUL 3 0A1 C10 H13 N O3 FORMUL 3 3WX C6 H11 N O2 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *344(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 LEU A 135 1 6 HELIX 5 AA5 PRO B 155 THR B 162 1 8 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 SER B 419 1 13 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 LEU B 250 SHEET 4 AA3 7 LEU B 283 LEU B 287 1 O LEU B 286 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 3 ILE B 368 ALA B 371 0 SHEET 2 AA5 3 PHE B 379 GLN B 382 -1 O GLN B 382 N ILE B 368 SHEET 3 AA5 3 APD I 4 FTR I 5 -1 O FTR I 5 N PHE B 379 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 SSBOND 1 CYS B 223 CYS B 255 1555 1555 2.05 SSBOND 2 CYS B 323 CYS B 358 1555 1555 2.05 SSBOND 3 CYS B 375 CYS B 378 1555 1555 2.05 LINK C Z9J I 1 N ALA I 2 1555 1555 1.33 LINK N Z9J I 1 C 3WX I 9 1555 1555 1.34 LINK C ALA I 2 N DAL I 3 1555 1555 1.33 LINK C DAL I 3 N APD I 4 1555 1555 1.33 LINK C APD I 4 N FTR I 5 1555 1555 1.33 LINK C5 APD I 4 NE2 GLN I 6 1555 1555 1.41 LINK C FTR I 5 N GLN I 6 1555 1555 1.33 LINK C THR I 7 N 0A1 I 8 1555 1555 1.34 LINK C 0A1 I 8 N 3WX I 9 1555 1555 1.36 CISPEP 1 SER B 326 PRO B 327 0 0.23 SITE 1 AC1 9 THR A 63 PHE A 64 HOH A 320 HOH A 337 SITE 2 AC1 9 SER B 178 LEU B 179 GLU B 181 VAL B 280 SITE 3 AC1 9 GLY B 281 SITE 1 AC2 10 SER B 153 ILE B 154 PRO B 155 ASP B 238 SITE 2 AC2 10 PHE B 379 ALA I 2 FTR I 5 THR I 7 SITE 3 AC2 10 HOH I 101 HOH I 103 SITE 1 AC3 11 ILE B 369 SER B 372 ASP B 374 CYS B 378 SITE 2 AC3 11 PHE B 379 VAL B 380 SER B 381 HOH B 519 SITE 3 AC3 11 DAL I 3 GLN I 6 THR I 7 CRYST1 70.875 70.875 166.304 90.00 90.00 120.00 P 31 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 0.014109 0.008146 0.000000 0.00000 SCALE2 0.000000 0.016292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006013 0.00000