PDB Short entry for 2QTW HEADER HYDROLASE 02-AUG-07 2QTW TITLE THE CRYSTAL STRUCTURE OF PCSK9 AT 1.9 ANGSTROMS RESOLUTION REVEALS TITLE 2 STRUCTURAL HOMOLOGY TO RESISTIN WITHIN THE C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 PROPEPTIDE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-152; COMPND 5 SYNONYM: PROPROTEIN CONVERTASE PC9, SUBTILISIN/KEXIN-LIKE PROTEASE COMPND 6 PC9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1; 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 FRAGMENT: UNP RESIDUES 153-692; COMPND 13 SYNONYM: PROPROTEIN CONVERTASE PC9, SUBTILISIN/KEXIN-LIKE PROTEASE COMPND 14 PC9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1; COMPND 15 EC: 3.4.21.-; COMPND 16 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; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 OTHER_DETAILS: FREESTYLE 293; 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; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 18 OTHER_DETAILS: FREESTYLE 293 KEYWDS PRO-PROTEIN CONVERTASE, CORONARY HEART DISEASE, HYPERCHOLESTEROLEMIA, KEYWDS 2 LOW DENSITY LIPOPROTEIN RECEPTOR, AUTOCATALYTIC CLEAVAGE, KEYWDS 3 CHOLESTEROL METABOLISM, DISEASE MUTATION, GLYCOPROTEIN, HYDROLASE, KEYWDS 4 LIPID METABOLISM, PHOSPHORYLATION, PROTEASE, SECRETED, SERINE KEYWDS 5 PROTEASE, STEROID METABOLISM, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR E.N.HAMPTON,M.W.KNUTH,J.LI,J.L.HARRIS,S.A.LESLEY,G.SPRAGGON REVDAT 8 29-JUL-20 2QTW 1 COMPND REMARK HETNAM LINK REVDAT 8 2 1 SITE REVDAT 7 05-FEB-20 2QTW 1 SOURCE SEQADV LINK REVDAT 6 18-SEP-13 2QTW 1 REMARK REVDAT 5 13-JUL-11 2QTW 1 VERSN REVDAT 4 24-FEB-09 2QTW 1 VERSN REVDAT 3 19-FEB-08 2QTW 1 JRNL REVDAT 2 25-SEP-07 2QTW 1 TITLE REVDAT 1 18-SEP-07 2QTW 0 JRNL AUTH E.N.HAMPTON,M.W.KNUTH,J.LI,J.L.HARRIS,S.A.LESLEY,G.SPRAGGON JRNL TITL THE SELF-INHIBITED STRUCTURE OF FULL-LENGTH PCSK9 AT 1.9 A JRNL TITL 2 REVEALS STRUCTURAL HOMOLOGY WITH RESISTIN WITHIN THE JRNL TITL 3 C-TERMINAL DOMAIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 14604 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17804797 JRNL DOI 10.1073/PNAS.0703402104 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49516 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2654 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3651 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4347 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.34000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 1.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.436 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4455 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3013 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6051 ; 1.490 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7280 ; 0.902 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 569 ; 6.843 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;33.120 ;22.903 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 707 ;14.412 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;17.969 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 693 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4972 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 888 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 967 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3375 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2138 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2577 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 332 ; 0.194 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.175 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 21 ; 0.099 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 86 ; 0.247 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.225 ; 0.200 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): 2939 ; 1.598 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1174 ; 0.356 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4583 ; 2.604 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1690 ; 4.032 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1468 ; 6.216 ; 8.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2QTW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000044049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 10.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52284 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.69900 REMARK 200 R SYM FOR SHELL (I) : 0.69900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG6000, 0.2M SODIUM CHLORIDE, PH REMARK 280 10.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, PH 10.50 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 31.21350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.29500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.07450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.29500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.21350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.07450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 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 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 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 465 HIS B 693 REMARK 465 HIS B 694 REMARK 465 HIS B 695 REMARK 465 HIS B 696 REMARK 465 HIS B 697 REMARK 465 HIS B 698 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 SG CYS A 67 O HOH B 1256 2.04 REMARK 500 O THR B 437 O HOH B 1167 2.15 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 OH TYR A 78 OE2 GLU B 405 3655 2.17 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 CYS B 654 CB CYS B 654 SG -0.102 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 LEU B 179 CA - CB - CG ANGL. DEV. = 14.8 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 HIS A 139 -4.54 73.51 REMARK 500 ASP B 186 -156.96 -162.62 REMARK 500 GLU B 197 124.30 -31.89 REMARK 500 ALA B 242 73.55 -111.93 REMARK 500 VAL B 280 -148.34 -126.87 REMARK 500 LEU B 351 -139.73 -117.36 REMARK 500 GLN B 503 113.97 -169.82 REMARK 500 SER B 545 -89.91 76.26 REMARK 500 PRO B 585 127.11 -36.66 REMARK 500 ASP B 651 -114.69 55.88 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 -107.16 REMARK 500 LYS B 494 ARG B 495 -149.82 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 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 330 O REMARK 620 2 VAL B 333 O 69.9 REMARK 620 3 THR B 335 OG1 99.5 82.9 REMARK 620 4 CYS B 358 O 137.2 144.5 71.5 REMARK 620 5 ASP B 360 OD2 138.0 70.4 88.4 84.4 REMARK 620 6 HOH B1231 O 51.1 119.5 93.6 87.1 170.1 REMARK 620 N 1 2 3 4 5 DBREF 2QTW A 29 152 UNP Q8NBP7 PCSK9_HUMAN 29 152 DBREF 2QTW B 153 692 UNP Q8NBP7 PCSK9_HUMAN 153 692 SEQADV 2QTW HIS B 693 UNP Q8NBP7 EXPRESSION TAG SEQADV 2QTW HIS B 694 UNP Q8NBP7 EXPRESSION TAG SEQADV 2QTW HIS B 695 UNP Q8NBP7 EXPRESSION TAG SEQADV 2QTW HIS B 696 UNP Q8NBP7 EXPRESSION TAG SEQADV 2QTW HIS B 697 UNP Q8NBP7 EXPRESSION TAG SEQADV 2QTW HIS B 698 UNP Q8NBP7 EXPRESSION TAG SEQRES 1 A 124 ARG ALA GLN GLU ASP GLU ASP GLY ASP TYR GLU GLU LEU SEQRES 2 A 124 VAL LEU ALA LEU ARG SER GLU GLU ASP GLY LEU ALA GLU SEQRES 3 A 124 ALA PRO GLU HIS GLY THR THR ALA THR PHE HIS ARG CYS SEQRES 4 A 124 ALA LYS ASP PRO TRP ARG LEU PRO GLY THR TYR VAL VAL SEQRES 5 A 124 VAL LEU LYS GLU GLU THR HIS LEU SER GLN SER GLU ARG SEQRES 6 A 124 THR ALA ARG ARG LEU GLN ALA GLN ALA ALA ARG ARG GLY SEQRES 7 A 124 TYR LEU THR LYS ILE LEU HIS VAL PHE HIS GLY LEU LEU SEQRES 8 A 124 PRO GLY PHE LEU VAL LYS MET SER GLY ASP LEU LEU GLU SEQRES 9 A 124 LEU ALA LEU LYS LEU PRO HIS VAL ASP TYR ILE GLU GLU SEQRES 10 A 124 ASP SER SER VAL PHE ALA GLN SEQRES 1 B 546 SER ILE PRO TRP ASN LEU GLU ARG ILE THR PRO PRO ARG SEQRES 2 B 546 TYR ARG ALA ASP GLU TYR GLN PRO PRO ASP GLY GLY SER SEQRES 3 B 546 LEU VAL GLU VAL TYR LEU LEU ASP THR SER ILE GLN SER SEQRES 4 B 546 ASP HIS ARG GLU ILE GLU GLY ARG VAL MET VAL THR ASP SEQRES 5 B 546 PHE GLU ASN VAL PRO GLU GLU ASP GLY THR ARG PHE HIS SEQRES 6 B 546 ARG GLN ALA SER LYS CYS ASP SER HIS GLY THR HIS LEU SEQRES 7 B 546 ALA GLY VAL VAL SER GLY ARG ASP ALA GLY VAL ALA LYS SEQRES 8 B 546 GLY ALA SER MET ARG SER LEU ARG VAL LEU ASN CYS GLN SEQRES 9 B 546 GLY LYS GLY THR VAL SER GLY THR LEU ILE GLY LEU GLU SEQRES 10 B 546 PHE ILE ARG LYS SER GLN LEU VAL GLN PRO VAL GLY PRO SEQRES 11 B 546 LEU VAL VAL LEU LEU PRO LEU ALA GLY GLY TYR SER ARG SEQRES 12 B 546 VAL LEU ASN ALA ALA CYS GLN ARG LEU ALA ARG ALA GLY SEQRES 13 B 546 VAL VAL LEU VAL THR ALA ALA GLY ASN PHE ARG ASP ASP SEQRES 14 B 546 ALA CYS LEU TYR SER PRO ALA SER ALA PRO GLU VAL ILE SEQRES 15 B 546 THR VAL GLY ALA THR ASN ALA GLN ASP GLN PRO VAL THR SEQRES 16 B 546 LEU GLY THR LEU GLY THR ASN PHE GLY ARG CYS VAL ASP SEQRES 17 B 546 LEU PHE ALA PRO GLY GLU ASP ILE ILE GLY ALA SER SER SEQRES 18 B 546 ASP CYS SER THR CYS PHE VAL SER GLN SER GLY THR SER SEQRES 19 B 546 GLN ALA ALA ALA HIS VAL ALA GLY ILE ALA ALA MET MET SEQRES 20 B 546 LEU SER ALA GLU PRO GLU LEU THR LEU ALA GLU LEU ARG SEQRES 21 B 546 GLN ARG LEU ILE HIS PHE SER ALA LYS ASP VAL ILE ASN SEQRES 22 B 546 GLU ALA TRP PHE PRO GLU ASP GLN ARG VAL LEU THR PRO SEQRES 23 B 546 ASN LEU VAL ALA ALA LEU PRO PRO SER THR HIS GLY ALA SEQRES 24 B 546 GLY TRP GLN LEU PHE CYS ARG THR VAL TRP SER ALA HIS SEQRES 25 B 546 SER GLY PRO THR ARG MET ALA THR ALA ILE ALA ARG CYS SEQRES 26 B 546 ALA PRO ASP GLU GLU LEU LEU SER CYS SER SER PHE SER SEQRES 27 B 546 ARG SER GLY LYS ARG ARG GLY GLU ARG MET GLU ALA GLN SEQRES 28 B 546 GLY GLY LYS LEU VAL CYS ARG ALA HIS ASN ALA PHE GLY SEQRES 29 B 546 GLY GLU GLY VAL TYR ALA ILE ALA ARG CYS CYS LEU LEU SEQRES 30 B 546 PRO GLN ALA ASN CYS SER VAL HIS THR ALA PRO PRO ALA SEQRES 31 B 546 GLU ALA SER MET GLY THR ARG VAL HIS CYS HIS GLN GLN SEQRES 32 B 546 GLY HIS VAL LEU THR GLY CYS SER SER HIS TRP GLU VAL SEQRES 33 B 546 GLU ASP LEU GLY THR HIS LYS PRO PRO VAL LEU ARG PRO SEQRES 34 B 546 ARG GLY GLN PRO ASN GLN CYS VAL GLY HIS ARG GLU ALA SEQRES 35 B 546 SER ILE HIS ALA SER CYS CYS HIS ALA PRO GLY LEU GLU SEQRES 36 B 546 CYS LYS VAL LYS GLU HIS GLY ILE PRO ALA PRO GLN GLU SEQRES 37 B 546 GLN VAL THR VAL ALA CYS GLU GLU GLY TRP THR LEU THR SEQRES 38 B 546 GLY CYS SER ALA LEU PRO GLY THR SER HIS VAL LEU GLY SEQRES 39 B 546 ALA TYR ALA VAL ASP ASN THR CYS VAL VAL ARG SER ARG SEQRES 40 B 546 ASP VAL SER THR THR GLY SER THR SER GLU GLU ALA VAL SEQRES 41 B 546 THR ALA VAL ALA ILE CYS CYS ARG SER ARG HIS LEU ALA SEQRES 42 B 546 GLN ALA SER GLN GLU LEU GLN HIS HIS HIS HIS HIS HIS MODRES 2QTW ASN B 533 ASN GLYCOSYLATION SITE HET NAG B1001 14 HET CA B 1 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION FORMUL 3 NAG C8 H15 N O6 FORMUL 4 CA CA 2+ FORMUL 5 HOH *320(H2 O) HELIX 1 1 LYS A 69 PRO A 71 5 3 HELIX 2 2 HIS A 87 ARG A 105 1 19 HELIX 3 3 SER A 127 ASP A 129 5 3 HELIX 4 4 LEU A 130 LYS A 136 1 7 HELIX 5 5 PRO B 155 ILE B 161 1 7 HELIX 6 6 ASP B 224 GLY B 236 1 13 HELIX 7 7 VAL B 261 GLN B 278 1 18 HELIX 8 8 SER B 294 ALA B 307 1 14 HELIX 9 9 ASP B 321 CYS B 323 5 3 HELIX 10 10 GLY B 384 GLU B 403 1 20 HELIX 11 11 THR B 407 PHE B 418 1 12 HELIX 12 12 ASN B 425 PHE B 429 5 5 HELIX 13 13 PRO B 430 ARG B 434 5 5 SHEET 1 A 3 THR A 63 HIS A 65 0 SHEET 2 A 3 VAL A 140 ALA A 151 1 O ILE A 143 N THR A 63 SHEET 3 A 3 LYS B 258 THR B 260 -1 O GLY B 259 N VAL A 149 SHEET 1 B 6 LYS A 110 PHE A 115 0 SHEET 2 B 6 GLY A 121 LYS A 125 -1 O LYS A 125 N LYS A 110 SHEET 3 B 6 ARG A 73 LEU A 82 -1 N VAL A 80 O PHE A 122 SHEET 4 B 6 VAL A 140 ALA A 151 -1 O TYR A 142 N VAL A 81 SHEET 5 B 6 LEU B 289 GLY B 292 -1 O ALA B 290 N PHE A 150 SHEET 6 B 6 TYR B 325 SER B 326 -1 O SER B 326 N GLY B 291 SHEET 1 C 7 VAL B 200 GLU B 206 0 SHEET 2 C 7 SER B 246 ARG B 251 1 O MET B 247 N MET B 201 SHEET 3 C 7 GLU B 181 ASP B 186 1 N LEU B 184 O LEU B 250 SHEET 4 C 7 LEU B 283 LEU B 287 1 O VAL B 284 N TYR B 183 SHEET 5 C 7 VAL B 310 ALA B 314 1 O VAL B 310 N VAL B 285 SHEET 6 C 7 ILE B 334 THR B 339 1 O ILE B 334 N LEU B 311 SHEET 7 C 7 LEU B 361 PRO B 364 1 O LEU B 361 N GLY B 337 SHEET 1 D 2 THR B 347 LEU B 348 0 SHEET 2 D 2 LEU B 351 GLY B 352 -1 O LEU B 351 N LEU B 348 SHEET 1 E 2 ILE B 368 ALA B 371 0 SHEET 2 E 2 PHE B 379 GLN B 382 -1 O GLN B 382 N ILE B 368 SHEET 1 F 2 ALA B 420 LYS B 421 0 SHEET 2 F 2 LEU B 440 VAL B 441 -1 O VAL B 441 N ALA B 420 SHEET 1 G 3 PHE B 456 TRP B 461 0 SHEET 2 G 3 TYR B 521 LEU B 528 -1 O ALA B 524 N VAL B 460 SHEET 3 G 3 GLU B 482 PHE B 489 -1 N GLU B 482 O CYS B 527 SHEET 1 H 3 THR B 472 ALA B 475 0 SHEET 2 H 3 LYS B 506 ASN B 513 -1 O ALA B 511 N ALA B 473 SHEET 3 H 3 ARG B 495 GLN B 503 -1 N ARG B 499 O ARG B 510 SHEET 1 I 3 ASN B 533 ALA B 539 0 SHEET 2 I 3 SER B 595 HIS B 602 -1 O HIS B 602 N ASN B 533 SHEET 3 I 3 VAL B 558 HIS B 565 -1 N SER B 563 O HIS B 597 SHEET 1 J 2 THR B 548 HIS B 551 0 SHEET 2 J 2 GLN B 587 GLY B 590 -1 O GLY B 590 N THR B 548 SHEET 1 K 3 LEU B 606 ILE B 615 0 SHEET 2 K 3 VAL B 672 SER B 681 -1 O ALA B 676 N LYS B 611 SHEET 3 K 3 THR B 631 ALA B 637 -1 N THR B 631 O CYS B 679 SHEET 1 L 3 GLN B 621 ALA B 625 0 SHEET 2 L 3 THR B 653 SER B 658 -1 O CYS B 654 N VAL B 624 SHEET 3 L 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 2.08 SSBOND 2 CYS B 323 CYS B 358 1555 1555 2.13 SSBOND 3 CYS B 375 CYS B 378 1555 1555 2.07 SSBOND 4 CYS B 457 CYS B 527 1555 1555 2.05 SSBOND 5 CYS B 477 CYS B 526 1555 1555 2.03 SSBOND 6 CYS B 486 CYS B 509 1555 1555 1.99 SSBOND 7 CYS B 534 CYS B 601 1555 1555 2.06 SSBOND 8 CYS B 552 CYS B 600 1555 1555 2.01 SSBOND 9 CYS B 562 CYS B 588 1555 1555 2.05 SSBOND 10 CYS B 608 CYS B 679 1555 1555 2.04 SSBOND 11 CYS B 626 CYS B 678 1555 1555 2.03 SSBOND 12 CYS B 635 CYS B 654 1555 1555 2.06 LINK ND2 ASN B 533 C1 NAG B1001 1555 1555 1.45 LINK CA CA B 1 O ALA B 330 1555 1555 3.33 LINK CA CA B 1 O VAL B 333 1555 1555 2.63 LINK CA CA B 1 OG1 THR B 335 1555 1555 2.63 LINK CA CA B 1 O CYS B 358 1555 1555 3.07 LINK CA CA B 1 OD2 ASP B 360 1555 1555 2.85 LINK CA CA B 1 O HOH B1231 1555 1555 2.24 CISPEP 1 SER B 326 PRO B 327 0 -1.71 CRYST1 62.427 70.149 148.590 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 0.016019 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006730 0.00000