HEADER LIPID TRANSPORT 11-DEC-18 6NCO TITLE FRAGMENT-BASED DISCOVERY OF AN APOE4 STABILIZER COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APO-E; COMPND 5 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: APOE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID BINDING, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.G.JAKOB,W.QIU REVDAT 3 11-OCT-23 6NCO 1 REMARK REVDAT 2 08-MAY-19 6NCO 1 JRNL REVDAT 1 17-APR-19 6NCO 0 JRNL AUTH A.M.PETROS,A.KOREPANOVA,C.G.JAKOB,W.QIU,S.C.PANCHAL,J.WANG, JRNL AUTH 2 J.D.DIETRICH,J.T.BREWER,F.POHLKI,A.KLING,K.WILCOX,V.LAKICS, JRNL AUTH 3 L.BAHNASSAWY,P.REINHARDT,S.K.PARTHA,P.M.BODELLE,M.LAKE, JRNL AUTH 4 E.I.CHARYCH,V.S.STOLL,C.SUN,E.G.MOHLER JRNL TITL FRAGMENT-BASED DISCOVERY OF AN APOLIPOPROTEIN E4 (APOE4) JRNL TITL 2 STABILIZER. JRNL REF J.MED.CHEM. V. 62 4120 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 30933499 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00178 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20914 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1007 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 33.4685 - 3.2466 0.99 3065 133 0.1787 0.1884 REMARK 3 2 3.2466 - 2.5773 1.00 2893 160 0.1966 0.2248 REMARK 3 3 2.5773 - 2.2516 1.00 2935 129 0.1821 0.2005 REMARK 3 4 2.2516 - 2.0457 1.00 2863 156 0.1937 0.2407 REMARK 3 5 2.0457 - 1.8991 1.00 2881 146 0.2081 0.2533 REMARK 3 6 1.8991 - 1.7871 1.00 2838 144 0.2315 0.2763 REMARK 3 7 1.7871 - 1.6977 0.95 2712 149 0.3330 0.4204 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.520 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 : 0.007 1268 REMARK 3 ANGLE : 1.293 1719 REMARK 3 CHIRALITY : 0.283 187 REMARK 3 PLANARITY : 0.004 223 REMARK 3 DIHEDRAL : 8.156 1087 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 6NCO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000238504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-18 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) : 1.000 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 : NULL REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20917 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.707 REMARK 200 RESOLUTION RANGE LOW (A) : 45.105 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 1GS9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER MESYLATE 5,000; 0.1M BIS-TRIS BUFFER AT PH6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 20.48000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.48000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.43500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 LYS A 1 REMARK 465 VAL A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 ALA A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 7 REMARK 465 THR A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 PRO A 12 REMARK 465 GLU A 13 REMARK 465 LEU A 14 REMARK 465 ARG A 15 REMARK 465 GLN A 16 REMARK 465 GLN A 17 REMARK 465 THR A 18 REMARK 465 GLU A 19 REMARK 465 TRP A 20 REMARK 465 GLN A 21 REMARK 465 SER A 22 REMARK 465 GLY A 23 REMARK 465 GLY A 165 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KQP A 201 DBREF 6NCO A 1 162 UNP P02649 APOE_HUMAN 20 181 SEQADV 6NCO GLY A -19 UNP P02649 EXPRESSION TAG SEQADV 6NCO SER A -18 UNP P02649 EXPRESSION TAG SEQADV 6NCO SER A -17 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -16 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -15 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -14 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -13 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -12 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -11 UNP P02649 EXPRESSION TAG SEQADV 6NCO SER A -10 UNP P02649 EXPRESSION TAG SEQADV 6NCO SER A -9 UNP P02649 EXPRESSION TAG SEQADV 6NCO GLY A -8 UNP P02649 EXPRESSION TAG SEQADV 6NCO LEU A -7 UNP P02649 EXPRESSION TAG SEQADV 6NCO VAL A -6 UNP P02649 EXPRESSION TAG SEQADV 6NCO PRO A -5 UNP P02649 EXPRESSION TAG SEQADV 6NCO ARG A -4 UNP P02649 EXPRESSION TAG SEQADV 6NCO GLY A -3 UNP P02649 EXPRESSION TAG SEQADV 6NCO SER A -2 UNP P02649 EXPRESSION TAG SEQADV 6NCO HIS A -1 UNP P02649 EXPRESSION TAG SEQADV 6NCO MET A 0 UNP P02649 EXPRESSION TAG SEQADV 6NCO ARG A 112 UNP P02649 CYS 131 VARIANT SEQADV 6NCO GLN A 163 UNP P02649 EXPRESSION TAG SEQADV 6NCO ALA A 164 UNP P02649 EXPRESSION TAG SEQADV 6NCO GLY A 165 UNP P02649 EXPRESSION TAG SEQRES 1 A 185 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 185 VAL PRO ARG GLY SER HIS MET LYS VAL GLU GLN ALA VAL SEQRES 3 A 185 GLU THR GLU PRO GLU PRO GLU LEU ARG GLN GLN THR GLU SEQRES 4 A 185 TRP GLN SER GLY GLN ARG TRP GLU LEU ALA LEU GLY ARG SEQRES 5 A 185 PHE TRP ASP TYR LEU ARG TRP VAL GLN THR LEU SER GLU SEQRES 6 A 185 GLN VAL GLN GLU GLU LEU LEU SER SER GLN VAL THR GLN SEQRES 7 A 185 GLU LEU ARG ALA LEU MET ASP GLU THR MET LYS GLU LEU SEQRES 8 A 185 LYS ALA TYR LYS SER GLU LEU GLU GLU GLN LEU THR PRO SEQRES 9 A 185 VAL ALA GLU GLU THR ARG ALA ARG LEU SER LYS GLU LEU SEQRES 10 A 185 GLN ALA ALA GLN ALA ARG LEU GLY ALA ASP MET GLU ASP SEQRES 11 A 185 VAL ARG GLY ARG LEU VAL GLN TYR ARG GLY GLU VAL GLN SEQRES 12 A 185 ALA MET LEU GLY GLN SER THR GLU GLU LEU ARG VAL ARG SEQRES 13 A 185 LEU ALA SER HIS LEU ARG LYS LEU ARG LYS ARG LEU LEU SEQRES 14 A 185 ARG ASP ALA ASP ASP LEU GLN LYS ARG LEU ALA VAL TYR SEQRES 15 A 185 GLN ALA GLY HET KQP A 201 24 HETNAM KQP 1-[5-CHLORO-4'-(2-HYDROXYPROPAN-2-YL)[1,1'-BIPHENYL]-3- HETNAM 2 KQP YL]CYCLOBUTANE-1-CARBOXIMIDAMIDE FORMUL 2 KQP C20 H23 CL N2 O FORMUL 3 HOH *151(H2 O) HELIX 1 AA1 GLN A 24 LEU A 43 1 20 HELIX 2 AA2 SER A 44 LEU A 52 1 9 HELIX 3 AA3 SER A 54 GLU A 79 1 26 HELIX 4 AA4 ALA A 86 MET A 125 1 40 HELIX 5 AA5 THR A 130 GLN A 163 1 34 SITE 1 AC1 11 GLU A 27 LEU A 30 GLY A 31 TRP A 34 SITE 2 AC1 11 ASP A 35 GLU A 131 ARG A 134 LEU A 149 SITE 3 AC1 11 ASP A 153 GLN A 156 HOH A 374 CRYST1 40.960 52.870 86.440 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 0.024414 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011569 0.00000