HEADER HYDROLASE 17-DEC-08 3FKT TITLE CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH TITLE 2 SPIROPIPERDINE IMINOHYDANTOIN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEASE DOMAIN (RESIDUES 43-446); COMPND 5 SYNONYM: BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA- COMPND 6 SITE APP CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, COMPND 7 MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2; COMPND 8 EC: 3.4.23.46; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BACE, BACE1, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ASPARTYL PROTEASE, BACE, ALTERNATIVE SPLICING, GLYCOPROTEIN, KEYWDS 2 HYDROLASE, MEMBRANE, POLYMORPHISM, PROTEASE, TRANSMEMBRANE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR S.MUNSHI REVDAT 5 30-OCT-24 3FKT 1 REMARK REVDAT 4 06-SEP-23 3FKT 1 REMARK REVDAT 3 20-OCT-21 3FKT 1 REMARK SEQADV REVDAT 2 04-APR-18 3FKT 1 REMARK REVDAT 1 20-JAN-09 3FKT 0 SPRSDE 20-JAN-09 3FKT 3E3W JRNL AUTH J.C.BARROW,S.R.STAUFFER,K.E.RITTLE,P.L.NGO,M.S.YANG, JRNL AUTH 2 S.GRAHAM,G.MCGAUGHEY,K.HOLLOWAY,S.K.TUGUSHEVA,M.LAI, JRNL AUTH 3 A.S.ESPESETH,M.XU,Q.HUANG,P.ZUCK,D.A.LEVORSE,D.HAZUDA, JRNL AUTH 4 J.P.VACCA JRNL TITL DISCOVERY AND X-RAY CRYSTALLOGRAPHIC ANALYSIS OF A JRNL TITL 2 IMINOHYDANTOIN INHIBITOR OF BETA-SECRETASE JRNL REF J.MED.CHEM. V. 51 6259 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18811140 JRNL DOI 10.1021/JM800914N 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) : 42.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 38567 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2034 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) : 2796 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.3870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2883 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 342 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.00000 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): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.899 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3011 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4097 ; 1.438 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 368 ; 7.550 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;34.768 ;23.731 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 471 ;14.381 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.688 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 440 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2304 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1375 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2016 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 277 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 65 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.366 ; 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): 1881 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2962 ; 1.516 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1310 ; 2.109 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1135 ; 3.331 ; 4.500 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 : 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 3FKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050712. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5413 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : NULL 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56800 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 PACKAGE REMARK 200 STARTING MODEL: 1TQF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M LITHIUM SULFATE, 0.1M HEPES REMARK 280 BUFFER, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH REMARK 280 7.50. CRYSTALS WERE GROWN WITH L124671 AND SPIROPIPERDINE IMINOH REMARK 280 WAS BACK SOAKED IN THE CRYSTAL AT PH 5.0, PH 5.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.38400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.38400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 51.87150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.02100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.87150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.02100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.38400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.87150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.02100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.38400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.87150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.02100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 103.74300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 38.38400 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 A 709 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 PRO A 3 REMARK 465 ARG A 4 REMARK 465 GLU A 5 REMARK 465 THR A 6 REMARK 465 ASP A 7 REMARK 465 GLU A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 GLU A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 ARG A 15 REMARK 465 ARG A 16 REMARK 465 GLY A 178 REMARK 465 PHE A 179 REMARK 465 PRO A 180 REMARK 465 LEU A 181 REMARK 465 ASN A 182 REMARK 465 GLN A 183 REMARK 465 SER A 184 REMARK 465 GLU A 185 REMARK 465 VAL A 186 REMARK 465 LEU A 187 REMARK 465 ALA A 188 REMARK 465 SER A 189 REMARK 465 GLU A 330 REMARK 465 ASP A 331 REMARK 465 VAL A 332 REMARK 465 ALA A 333 REMARK 465 THR A 334 REMARK 465 HIS A 380 REMARK 465 VAL A 381 REMARK 465 TYR A 404 REMARK 465 ASN A 405 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 A 467 O HOH A 715 2.11 REMARK 500 OE2 GLU A 145 NH1 ARG A 215 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 O HOH A 518 O HOH A 518 3655 1.43 REMARK 500 O HOH A 637 O HOH A 747 3655 1.78 REMARK 500 O HOH A 716 O HOH A 716 3555 2.13 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 ASP A 243 N - CA - C ANGL. DEV. = -20.7 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 TRP A 217 -86.76 -142.77 REMARK 500 ASP A 243 -27.00 -178.75 REMARK 500 ALA A 292 125.14 -38.94 REMARK 500 ASP A 383 -164.25 -123.76 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 TYR A 242 ASP A 243 105.31 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 TYR A 242 11.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SII A 406 DBREF 3FKT A 2 405 UNP P56817 BACE1_HUMAN 43 446 SEQADV 3FKT MET A 1 UNP P56817 INITIATING METHIONINE SEQADV 3FKT ALA A 95 UNP P56817 LYS 136 ENGINEERED MUTATION SEQADV 3FKT ALA A 97 UNP P56817 GLU 138 ENGINEERED MUTATION SEQRES 1 A 405 MET LEU PRO ARG GLU THR ASP GLU GLU PRO GLU GLU PRO SEQRES 2 A 405 GLY ARG ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU SEQRES 3 A 405 ARG GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR SEQRES 4 A 405 VAL GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP SEQRES 5 A 405 THR GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS SEQRES 6 A 405 PRO PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER SEQRES 7 A 405 THR TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR SEQRES 8 A 405 THR GLN GLY ALA TRP ALA GLY GLU LEU GLY THR ASP LEU SEQRES 9 A 405 VAL SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA SEQRES 10 A 405 ASN ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE SEQRES 11 A 405 ASN GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR SEQRES 12 A 405 ALA GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE SEQRES 13 A 405 PHE ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU SEQRES 14 A 405 PHE SER LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN SEQRES 15 A 405 GLN SER GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE SEQRES 16 A 405 ILE GLY GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU SEQRES 17 A 405 TRP TYR THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL SEQRES 18 A 405 ILE ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS SEQRES 19 A 405 MET ASP CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL SEQRES 20 A 405 ASP SER GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL SEQRES 21 A 405 PHE GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER SEQRES 22 A 405 THR GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN SEQRES 23 A 405 LEU VAL CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE SEQRES 24 A 405 PHE PRO VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR SEQRES 25 A 405 ASN GLN SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR SEQRES 26 A 405 LEU ARG PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP SEQRES 27 A 405 CYS TYR LYS PHE ALA ILE SER GLN SER SER THR GLY THR SEQRES 28 A 405 VAL MET GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL SEQRES 29 A 405 PHE ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER SEQRES 30 A 405 ALA CYS HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL SEQRES 31 A 405 GLU GLY PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY SEQRES 32 A 405 TYR ASN HET SII A 406 36 HETNAM SII N-(4-{[4-(CYCLOHEXYLAMINO)-1-(3-FLUOROPHENYL)-2-OXO-1, HETNAM 2 SII 3,8-TRIAZASPIRO[4.5]DEC-3-EN-8-YL]METHYL}PHENYL) HETNAM 3 SII ACETAMIDE FORMUL 2 SII C28 H34 F N5 O2 FORMUL 3 HOH *342(H2 O) HELIX 1 1 PHE A 19 VAL A 23 5 5 HELIX 2 2 GLN A 73 SER A 77 5 5 HELIX 3 3 TYR A 143 ALA A 147 5 5 HELIX 4 4 PRO A 155 THR A 164 1 10 HELIX 5 5 ASP A 200 SER A 202 5 3 HELIX 6 6 ASP A 236 ASN A 241 1 6 HELIX 7 7 LYS A 258 SER A 272 1 15 HELIX 8 8 PRO A 278 LEU A 283 1 6 HELIX 9 9 PRO A 296 PHE A 300 5 5 HELIX 10 10 LEU A 321 TYR A 325 1 5 HELIX 11 11 GLY A 354 GLU A 359 1 6 HELIX 12 12 ASP A 398 GLY A 403 5 6 SHEET 1 A 9 ARG A 81 PRO A 90 0 SHEET 2 A 9 ALA A 95 SER A 106 -1 O LEU A 100 N LYS A 85 SHEET 3 A 9 TYR A 34 VAL A 40 -1 N THR A 39 O SER A 106 SHEET 4 A 9 LEU A 26 GLY A 28 -1 N ARG A 27 O TYR A 35 SHEET 5 A 9 GLY A 191 ILE A 196 -1 O GLY A 192 N LEU A 26 SHEET 6 A 9 PHE A 170 CYS A 175 -1 N GLN A 173 O SER A 193 SHEET 7 A 9 PHE A 361 ASP A 366 -1 O VAL A 363 N LEU A 172 SHEET 8 A 9 ARG A 371 SER A 377 -1 O ALA A 375 N TYR A 362 SHEET 9 A 9 TYR A 204 PRO A 212 -1 N THR A 211 O ILE A 372 SHEET 1 B13 ARG A 81 PRO A 90 0 SHEET 2 B13 ALA A 95 SER A 106 -1 O LEU A 100 N LYS A 85 SHEET 3 B13 VAL A 115 ASP A 126 -1 O ALA A 121 N GLU A 99 SHEET 4 B13 PHE A 58 GLY A 61 1 N VAL A 60 O ILE A 122 SHEET 5 B13 GLY A 137 GLY A 140 -1 O ILE A 138 N ALA A 59 SHEET 6 B13 GLN A 45 ASP A 52 1 N LEU A 50 O LEU A 139 SHEET 7 B13 TYR A 34 VAL A 40 -1 N TYR A 34 O VAL A 51 SHEET 8 B13 LEU A 26 GLY A 28 -1 N ARG A 27 O TYR A 35 SHEET 9 B13 GLY A 191 ILE A 196 -1 O GLY A 192 N LEU A 26 SHEET 10 B13 PHE A 170 CYS A 175 -1 N GLN A 173 O SER A 193 SHEET 11 B13 PHE A 361 ASP A 366 -1 O VAL A 363 N LEU A 172 SHEET 12 B13 ARG A 371 SER A 377 -1 O ALA A 375 N TYR A 362 SHEET 13 B13 TYR A 204 PRO A 212 -1 N THR A 211 O ILE A 372 SHEET 1 C 5 GLU A 220 VAL A 221 0 SHEET 2 C 5 SER A 245 VAL A 247 -1 O SER A 245 N VAL A 221 SHEET 3 C 5 THR A 351 MET A 353 1 O MET A 353 N ILE A 246 SHEET 4 C 5 LEU A 254 PRO A 257 -1 N ARG A 255 O VAL A 352 SHEET 5 C 5 ILE A 344 SER A 347 1 O SER A 345 N LEU A 256 SHEET 1 D 5 GLN A 231 ASP A 232 0 SHEET 2 D 5 ILE A 223 ILE A 228 -1 N ILE A 228 O GLN A 231 SHEET 3 D 5 ILE A 303 MET A 308 -1 O TYR A 306 N ARG A 225 SHEET 4 D 5 GLN A 314 ILE A 320 -1 O ILE A 320 N ILE A 303 SHEET 5 D 5 ALA A 389 VAL A 395 -1 O GLU A 391 N ARG A 317 SHEET 1 E 3 VAL A 288 GLN A 291 0 SHEET 2 E 3 ASP A 337 PHE A 342 -1 O ASP A 338 N TRP A 290 SHEET 3 E 3 LEU A 326 PRO A 328 -1 N ARG A 327 O LYS A 341 SSBOND 1 CYS A 175 CYS A 379 1555 1555 2.04 SSBOND 2 CYS A 237 CYS A 402 1555 1555 2.05 SSBOND 3 CYS A 289 CYS A 339 1555 1555 2.02 CISPEP 1 SER A 42 PRO A 43 0 -7.24 CISPEP 2 SER A 42 PRO A 43 0 -3.67 CISPEP 3 ARG A 148 PRO A 149 0 2.89 CISPEP 4 GLY A 392 PRO A 393 0 -2.95 SITE 1 AC1 16 TYR A 91 THR A 92 GLN A 93 GLY A 94 SITE 2 AC1 16 LYS A 127 PHE A 128 ILE A 130 TYR A 218 SITE 3 AC1 16 LYS A 244 GLY A 250 THR A 251 THR A 349 SITE 4 AC1 16 VAL A 352 HOH A 433 HOH A 532 HOH A 631 CRYST1 103.743 128.042 76.768 90.00 90.00 90.00 C 2 2 21 8 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 0.009639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013026 0.00000