HEADER IMMUNE SYSTEM 18-JUL-18 6E4Z
TITLE ANTI-PCSK9 FAB 6E2 BOUND TO THE MODIFIED N-TERMINAL PEPTIDE FROM PCSK9
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 6E2 HEAVY CHAIN;
COMPND 3 CHAIN: H;
COMPND 4 FRAGMENT: FAB;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 6E2 LIGHT CHAIN;
COMPND 8 CHAIN: L;
COMPND 9 FRAGMENT: FAB;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9;
COMPND 13 CHAIN: P;
COMPND 14 FRAGMENT: UNP RESIDUES 32-53;
COMPND 15 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN
COMPND 16 CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9;
COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: 64B4;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBR322;
SOURCE 10 MOL_ID: 2;
SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 12 ORGANISM_COMMON: MOUSE;
SOURCE 13 ORGANISM_TAXID: 10090;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 16 EXPRESSION_SYSTEM_STRAIN: 64B4;
SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PBR322;
SOURCE 19 MOL_ID: 3;
SOURCE 20 SYNTHETIC: YES;
SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 22 ORGANISM_COMMON: HUMAN;
SOURCE 23 ORGANISM_TAXID: 9606
KEYWDS ANTIBODY, HYDROLASE, PCSK9, FAB COMPLEX, IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR M.H.ULTSCH,D.K.KIRCHHOFER
REVDAT 3 15-NOV-23 6E4Z 1 REMARK
REVDAT 2 11-OCT-23 6E4Z 1 LINK
REVDAT 1 10-APR-19 6E4Z 0
JRNL AUTH M.ULTSCH,W.LI,C.EIGENBROT,P.DI LELLO,M.T.LIPARI,S.GERHARDY,
JRNL AUTH 2 A.P.AHYOUNG,J.QUINN,Y.FRANKE,Y.CHEN,M.KONG BELTRAN,
JRNL AUTH 3 A.PETERSON,D.KIRCHHOFER
JRNL TITL IDENTIFICATION OF A HELICAL SEGMENT WITHIN THE INTRINSICALLY
JRNL TITL 2 DISORDERED REGION OF THE PCSK9 PRODOMAIN.
JRNL REF J. MOL. BIOL. V. 431 885 2019
JRNL REFN ESSN 1089-8638
JRNL PMID 30653992
JRNL DOI 10.1016/J.JMB.2018.11.025
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10.1-2155_2155: ???)
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.42
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 31636
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.236
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.350
REMARK 3 FREE R VALUE TEST SET COUNT : 1060
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 33.4204 - 4.4006 1.00 4013 143 0.1701 0.2141
REMARK 3 2 4.4006 - 3.4941 1.00 3850 156 0.1716 0.1973
REMARK 3 3 3.4941 - 3.0527 1.00 3837 132 0.2108 0.2802
REMARK 3 4 3.0527 - 2.7738 1.00 3806 128 0.2279 0.2680
REMARK 3 5 2.7738 - 2.5750 1.00 3808 134 0.2272 0.2780
REMARK 3 6 2.5750 - 2.4233 1.00 3775 126 0.2291 0.2657
REMARK 3 7 2.4233 - 2.3019 1.00 3780 122 0.2360 0.2725
REMARK 3 8 2.3019 - 2.2018 0.98 3707 119 0.2705 0.3134
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.270
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.700
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 : 0.020 3544
REMARK 3 ANGLE : 1.039 4808
REMARK 3 CHIRALITY : 0.054 535
REMARK 3 PLANARITY : 0.006 610
REMARK 3 DIHEDRAL : 13.541 2102
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: (CHAIN H AND RESID 1:114)
REMARK 3 ORIGIN FOR THE GROUP (A): 4.1883 36.6349 -12.4311
REMARK 3 T TENSOR
REMARK 3 T11: 0.3138 T22: 0.3082
REMARK 3 T33: 0.3698 T12: 0.0565
REMARK 3 T13: 0.1061 T23: 0.0250
REMARK 3 L TENSOR
REMARK 3 L11: 1.6675 L22: 2.0305
REMARK 3 L33: 2.1471 L12: 0.4564
REMARK 3 L13: 0.4533 L23: -0.2908
REMARK 3 S TENSOR
REMARK 3 S11: 0.0614 S12: 0.0832 S13: 0.1364
REMARK 3 S21: -0.2391 S22: 0.0325 S23: -0.2240
REMARK 3 S31: -0.0352 S32: 0.0865 S33: -0.0922
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: (CHAIN L AND RESID 1:107)
REMARK 3 ORIGIN FOR THE GROUP (A): -8.0920 17.7578 -11.5710
REMARK 3 T TENSOR
REMARK 3 T11: 0.3245 T22: 0.2802
REMARK 3 T33: 0.3545 T12: 0.0209
REMARK 3 T13: 0.0377 T23: 0.0078
REMARK 3 L TENSOR
REMARK 3 L11: 3.6952 L22: 3.2352
REMARK 3 L33: 2.7993 L12: 1.3720
REMARK 3 L13: -0.9464 L23: 0.2957
REMARK 3 S TENSOR
REMARK 3 S11: -0.0468 S12: 0.1777 S13: -0.4944
REMARK 3 S21: -0.1733 S22: -0.0428 S23: -0.1477
REMARK 3 S31: 0.4326 S32: -0.1677 S33: 0.0810
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: (CHAIN H AND RESID 115:214)
REMARK 3 ORIGIN FOR THE GROUP (A): -17.0998 41.3125 -38.5206
REMARK 3 T TENSOR
REMARK 3 T11: 0.9213 T22: 0.5940
REMARK 3 T33: 0.6674 T12: 0.0445
REMARK 3 T13: -0.2732 T23: -0.0675
REMARK 3 L TENSOR
REMARK 3 L11: 1.5855 L22: 1.7257
REMARK 3 L33: 1.5852 L12: 1.0438
REMARK 3 L13: 0.5809 L23: 0.1517
REMARK 3 S TENSOR
REMARK 3 S11: -0.2103 S12: 0.0688 S13: 0.5088
REMARK 3 S21: -0.8767 S22: 0.0388 S23: 0.9204
REMARK 3 S31: -0.4582 S32: -0.3542 S33: 0.1385
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: (CHAIN L AND RESID 108:213)
REMARK 3 ORIGIN FOR THE GROUP (A): -17.9583 26.8299 -46.8315
REMARK 3 T TENSOR
REMARK 3 T11: 0.9049 T22: 0.7632
REMARK 3 T33: 0.5271 T12: -0.0669
REMARK 3 T13: -0.1649 T23: 0.0031
REMARK 3 L TENSOR
REMARK 3 L11: 1.4008 L22: 1.8312
REMARK 3 L33: 2.1572 L12: 0.9508
REMARK 3 L13: -0.0687 L23: -0.0693
REMARK 3 S TENSOR
REMARK 3 S11: -0.2054 S12: 0.4616 S13: 0.1386
REMARK 3 S21: -0.5556 S22: 0.2705 S23: 0.1375
REMARK 3 S31: 0.0169 S32: -0.1925 S33: -0.0857
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: (CHAIN P)
REMARK 3 ORIGIN FOR THE GROUP (A): -1.9762 28.1307 5.1510
REMARK 3 T TENSOR
REMARK 3 T11: 0.4614 T22: 0.5224
REMARK 3 T33: 0.4065 T12: -0.0659
REMARK 3 T13: 0.0561 T23: 0.1066
REMARK 3 L TENSOR
REMARK 3 L11: 7.3526 L22: 5.1914
REMARK 3 L33: 8.1675 L12: 2.5370
REMARK 3 L13: 0.6708 L23: -0.2100
REMARK 3 S TENSOR
REMARK 3 S11: 0.0667 S12: -1.1774 S13: -0.7110
REMARK 3 S21: 0.8379 S22: -0.2388 S23: -0.3779
REMARK 3 S31: 0.2914 S32: -0.6654 S33: 0.1655
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 6E4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-18.
REMARK 100 THE DEPOSITION ID IS D_1000235724.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-ID
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 : DOUBLE CRYSTAL SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31726
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 33.420
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 7.300
REMARK 200 R MERGE (I) : 0.08200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 6.40
REMARK 200 R MERGE FOR SHELL (I) : 0.82700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.110
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: PDB ENTRY 6E4Y
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 58.99
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 15% W/V PEG8000, 0.2 M ZINC ACETATE,
REMARK 280 0.1 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X+1/2,Y+1/2,-Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 35.46450
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.89100
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.46450
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.89100
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: 5230 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -200.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, P
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 H 446 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 SER H 127
REMARK 465 SER H 128
REMARK 465 LYS H 129
REMARK 465 SER H 130
REMARK 465 THR H 131
REMARK 465 SER H 132
REMARK 465 GLY H 133
REMARK 465 GLY H 134
REMARK 465 SER H 215
REMARK 465 CYS H 216
REMARK 465 ASP H 217
REMARK 465 LYS H 218
REMARK 465 THR H 219
REMARK 465 HIS H 220
REMARK 465 THR H 221
REMARK 465 CYS L 214
REMARK 465 GLU P 32
REMARK 465 ASP P 33
REMARK 465 GLU P 34
REMARK 465 ASP P 50
REMARK 465 GLY P 51
REMARK 465 LEU P 52
REMARK 465 ALA P 53
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 OE1 GLU H 148 O HOH H 401 2.13
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 PHE H 27 115.28 -167.81
REMARK 500 ASP H 144 71.64 67.65
REMARK 500 SER H 161 -83.40 -61.77
REMARK 500 THR H 191 -85.03 -139.88
REMARK 500 GLN H 192 96.32 -66.76
REMARK 500 SER L 27E 54.20 -61.12
REMARK 500 ASN L 28 -154.62 -147.39
REMARK 500 MET L 51 -37.71 80.90
REMARK 500 ASN L 138 79.26 52.93
REMARK 500 LYS L 190 -60.94 -102.51
REMARK 500 SEP P 47 68.16 -158.97
REMARK 500 SEP P 47 63.34 -161.14
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 ZN H 301 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP H 53 OD1
REMARK 620 2 ASP L 60 OD1 72.3
REMARK 620 3 HOH L 446 O 107.0 112.6
REMARK 620 4 GLU P 48 OE2 117.5 47.8 110.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN L 301 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS H 164 NE2
REMARK 620 2 ASN L 137 OD1 101.3
REMARK 620 3 ASN L 138 OD1 89.6 78.7
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN L 304 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS L 27D NE2
REMARK 620 2 GLU P 49 OE2 73.0
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN L 303 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU L 81 OE1
REMARK 620 2 GLU L 81 OE2 66.3
REMARK 620 3 HOH L 438 O 79.9 138.5
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN L 302 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP L 185 OD2
REMARK 620 2 HIS L 189 NE2 118.6
REMARK 620 3 SO4 L 305 O1 100.9 105.4
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN H 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN L 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 L 305
DBREF 6E4Z H 1 221 PDB 6E4Z 6E4Z 1 221
DBREF 6E4Z L 1 106 PDB 6E4Z 6E4Z 1 106
DBREF1 6E4Z L 107 214 UNP A0A097PUG4_MOUSE
DBREF2 6E4Z L A0A097PUG4 131 238
DBREF 6E4Z P 32 53 UNP Q8NBP7 PCSK9_HUMAN 32 53
SEQRES 1 H 224 GLU VAL LYS LEU GLU GLU SER GLY GLY GLY LEU VAL GLN
SEQRES 2 H 224 PRO GLY GLY SER MET LYS LEU SER CYS VAL ALA SER ARG
SEQRES 3 H 224 PHE THR LEU SER LYS TYR TRP MET ASN TRP VAL ARG GLN
SEQRES 4 H 224 SER PRO GLU LYS GLY LEU GLU TRP VAL ALA GLN ILE ARG
SEQRES 5 H 224 LEU LYS SER ASP ASN TYR ALA THR NEP TYR ALA GLU SER
SEQRES 6 H 224 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASP SER LYS
SEQRES 7 H 224 SER SER VAL TYR LEU GLN MET ASN ASN LEU ARG ALA GLU
SEQRES 8 H 224 ASP THR GLY ILE TYR TYR CYS THR GLY GLU ILE PHE VAL
SEQRES 9 H 224 ASN TRP GLY GLN GLY THR LEU VAL THR VAL SER ALA ALA
SEQRES 10 H 224 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER
SEQRES 11 H 224 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS
SEQRES 12 H 224 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER
SEQRES 13 H 224 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE
SEQRES 14 H 224 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER
SEQRES 15 H 224 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN
SEQRES 16 H 224 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR
SEQRES 17 H 224 LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS ASP LYS
SEQRES 18 H 224 THR HIS THR
SEQRES 1 L 219 ASP ILE VAL MET THR GLN ALA ALA PRO SER VAL PRO VAL
SEQRES 2 L 219 THR PRO GLY GLU SER VAL SER ILE SER CYS ARG SER SER
SEQRES 3 L 219 LYS SER LEU LEU HIS SER ASN GLY ASN THR TYR LEU TYR
SEQRES 4 L 219 TRP PHE LEU GLN ARG PRO GLY GLN SER PRO GLN LEU LEU
SEQRES 5 L 219 ILE TYR ARG MET SER ASN LEU ALA SER GLY VAL PRO ASP
SEQRES 6 L 219 ARG PHE SER GLY SER GLY SER GLY THR ALA PHE THR LEU
SEQRES 7 L 219 ARG ILE SER ARG VAL GLU ALA GLU ASP VAL GLY VAL TYR
SEQRES 8 L 219 TYR CYS MET GLN HIS LEU GLU TYR PRO PHE THR PHE GLY
SEQRES 9 L 219 ALA GLY THR LYS LEU GLU LEU LYS ARG THR VAL ALA ALA
SEQRES 10 L 219 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU
SEQRES 11 L 219 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN
SEQRES 12 L 219 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP
SEQRES 13 L 219 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR
SEQRES 14 L 219 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER
SEQRES 15 L 219 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS
SEQRES 16 L 219 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER
SEQRES 17 L 219 PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS
SEQRES 1 P 22 GLU ASP GLU ASP GLY ASP TYS GLU GLU LEU VAL LEU ALA
SEQRES 2 P 22 LEU ARG SEP GLU GLU ASP GLY LEU ALA
MODRES 6E4Z TYS P 38 TYR MODIFIED RESIDUE
MODRES 6E4Z SEP P 47 SER MODIFIED RESIDUE
HET NEP H 58 14
HET HIP H 58 14
HET TYS P 38 16
HET SEP P 47 20
HET ZN H 301 1
HET ZN L 301 1
HET ZN L 302 1
HET ZN L 303 1
HET ZN L 304 1
HET SO4 L 305 5
HETNAM NEP N1-PHOSPHONOHISTIDINE
HETNAM HIP ND1-PHOSPHONOHISTIDINE
HETNAM TYS O-SULFO-L-TYROSINE
HETNAM SEP PHOSPHOSERINE
HETNAM ZN ZINC ION
HETNAM SO4 SULFATE ION
HETSYN SEP PHOSPHONOSERINE
FORMUL 1 NEP C6 H10 N3 O5 P
FORMUL 1 HIP C6 H11 N3 O5 P 1+
FORMUL 3 TYS C9 H11 N O6 S
FORMUL 3 SEP C3 H8 N O6 P
FORMUL 4 ZN 5(ZN 2+)
FORMUL 9 SO4 O4 S 2-
FORMUL 10 HOH *122(H2 O)
HELIX 1 AA1 THR H 28 TYR H 32 5 5
HELIX 2 AA2 LEU H 52A ASN H 54 5 5
HELIX 3 AA3 ASP H 73 LYS H 75 5 3
HELIX 4 AA4 ARG H 83 THR H 87 5 5
HELIX 5 AA5 SER H 156 ALA H 158 5 3
HELIX 6 AA6 LYS H 201 ASN H 204 5 4
HELIX 7 AA7 GLU L 79 VAL L 83 5 5
HELIX 8 AA8 SER L 121 GLY L 128 1 8
HELIX 9 AA9 LYS L 183 GLU L 187 1 5
HELIX 10 AB1 GLY P 36 ARG P 46 1 11
SHEET 1 AA1 4 LYS H 3 SER H 7 0
SHEET 2 AA1 4 MET H 18 SER H 25 -1 O SER H 25 N LYS H 3
SHEET 3 AA1 4 SER H 77 MET H 82 -1 O MET H 82 N MET H 18
SHEET 4 AA1 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81
SHEET 1 AA2 6 GLY H 10 VAL H 12 0
SHEET 2 AA2 6 THR H 107 VAL H 111 1 O THR H 110 N GLY H 10
SHEET 3 AA2 6 GLY H 88 THR H 93 -1 N GLY H 88 O VAL H 109
SHEET 4 AA2 6 MET H 34 SER H 40 -1 N VAL H 37 O TYR H 91
SHEET 5 AA2 6 GLY H 44 ILE H 51 -1 O GLU H 46 N ARG H 38
SHEET 6 AA2 6 THR H 57 TYR H 59 -1 O NEP H 58 N GLN H 50
SHEET 1 AA3 4 SER H 120 LEU H 124 0
SHEET 2 AA3 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122
SHEET 3 AA3 4 TYR H 176 VAL H 184 -1 O VAL H 182 N LEU H 138
SHEET 4 AA3 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181
SHEET 1 AA4 4 SER H 120 LEU H 124 0
SHEET 2 AA4 4 ALA H 136 TYR H 145 -1 O LEU H 141 N PHE H 122
SHEET 3 AA4 4 TYR H 176 VAL H 184 -1 O VAL H 182 N LEU H 138
SHEET 4 AA4 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177
SHEET 1 AA5 3 THR H 151 TRP H 154 0
SHEET 2 AA5 3 TYR H 194 HIS H 200 -1 O ASN H 199 N THR H 151
SHEET 3 AA5 3 THR H 205 VAL H 211 -1 O VAL H 211 N TYR H 194
SHEET 1 AA6 4 MET L 4 THR L 5 0
SHEET 2 AA6 4 VAL L 19 SER L 25 -1 O ARG L 24 N THR L 5
SHEET 3 AA6 4 ALA L 70 ILE L 75 -1 O LEU L 73 N ILE L 21
SHEET 4 AA6 4 PHE L 62 SER L 67 -1 N SER L 63 O ARG L 74
SHEET 1 AA7 6 SER L 10 VAL L 13 0
SHEET 2 AA7 6 THR L 102 LEU L 106 1 O GLU L 105 N VAL L 11
SHEET 3 AA7 6 GLY L 84 GLN L 90 -1 N GLY L 84 O LEU L 104
SHEET 4 AA7 6 LEU L 33 GLN L 38 -1 N TYR L 34 O MET L 89
SHEET 5 AA7 6 GLN L 45 TYR L 49 -1 O LEU L 47 N TRP L 35
SHEET 6 AA7 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49
SHEET 1 AA8 4 SER L 10 VAL L 13 0
SHEET 2 AA8 4 THR L 102 LEU L 106 1 O GLU L 105 N VAL L 11
SHEET 3 AA8 4 GLY L 84 GLN L 90 -1 N GLY L 84 O LEU L 104
SHEET 4 AA8 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90
SHEET 1 AA9 4 SER L 114 PHE L 118 0
SHEET 2 AA9 4 THR L 129 PHE L 139 -1 O ASN L 137 N SER L 114
SHEET 3 AA9 4 TYR L 173 SER L 182 -1 O LEU L 181 N ALA L 130
SHEET 4 AA9 4 SER L 159 VAL L 163 -1 N GLN L 160 O THR L 178
SHEET 1 AB1 4 ALA L 153 LEU L 154 0
SHEET 2 AB1 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153
SHEET 3 AB1 4 VAL L 191 THR L 197 -1 O ALA L 193 N LYS L 149
SHEET 4 AB1 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196
SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.06
SSBOND 2 CYS H 140 CYS H 196 1555 1555 2.04
SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.07
SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.03
LINK C THR H 57 N ANEP H 58 1555 1555 1.33
LINK C THR H 57 N BHIP H 58 1555 1555 1.33
LINK C ANEP H 58 N TYR H 59 1555 1555 1.33
LINK C BHIP H 58 N TYR H 59 1555 1555 1.33
LINK C ASP P 37 N TYS P 38 1555 1555 1.33
LINK C TYS P 38 N GLU P 39 1555 1555 1.33
LINK C ARG P 46 N ASEP P 47 1555 1555 1.33
LINK C ARG P 46 N BSEP P 47 1555 1555 1.33
LINK C ASEP P 47 N GLU P 48 1555 1555 1.33
LINK C BSEP P 47 N GLU P 48 1555 1555 1.33
LINK OD1 ASP H 53 ZN ZN H 301 1555 1555 1.95
LINK NE2 HIS H 164 ZN ZN L 301 1555 1555 2.07
LINK ZN ZN H 301 OD1 ASP L 60 4455 1555 1.89
LINK ZN ZN H 301 O HOH L 446 1555 4555 2.19
LINK ZN ZN H 301 OE2 GLU P 48 1555 1555 2.00
LINK NE2 HIS L 27D ZN ZN L 304 1555 1555 2.02
LINK OE1 GLU L 81 ZN ZN L 303 1555 1555 2.01
LINK OE2 GLU L 81 ZN ZN L 303 1555 1555 2.00
LINK OD1 ASN L 137 ZN ZN L 301 1555 1555 2.11
LINK OD1 ASN L 138 ZN ZN L 301 1555 1555 2.04
LINK OD2 ASP L 185 ZN ZN L 302 1555 1555 2.06
LINK NE2 HIS L 189 ZN ZN L 302 1555 1555 2.08
LINK ZN ZN L 302 O1 SO4 L 305 1555 1555 2.29
LINK ZN ZN L 303 O HOH L 438 1555 1555 2.59
LINK ZN ZN L 304 OE2 GLU P 49 1555 1555 2.01
CISPEP 1 PHE H 146 PRO H 147 0 -10.57
CISPEP 2 GLU H 148 PRO H 149 0 -0.59
CISPEP 3 TYR L 94 PRO L 95 0 -1.71
CISPEP 4 TYR L 140 PRO L 141 0 -0.29
SITE 1 AC1 4 ASP H 53 ASP L 60 HOH L 446 GLU P 48
SITE 1 AC2 4 HIS H 164 ASN L 137 ASN L 138 HOH L 414
SITE 1 AC3 3 ASP L 185 HIS L 189 SO4 L 305
SITE 1 AC4 2 GLU L 81 HOH L 438
SITE 1 AC5 4 HIS L 27D HOH L 442 SEP P 47 GLU P 49
SITE 1 AC6 4 GLN L 155 ASP L 185 HIS L 189 ZN L 302
CRYST1 70.929 99.782 86.328 90.00 90.00 90.00 P 21 21 2 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 0.014099 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010022 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011584 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
