HEADER HYDROLASE/INHIBITOR 27-SEP-17 5YGY TITLE CRYSTAL STRUCTURE OF BACE1 IN COMPLEX WITH (S)-N-(3-(2-AMINO-6- TITLE 2 (FLUOROMETHYL)-4 -METHYL-4H-1,3-OXAZIN-4-YL)-4-FLUOROPHENYL)-5- TITLE 3 CYANOPICOLINAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 43-454; COMPND 5 SYNONYM: ASPARTYL PROTEASE 2,ASP 2,BETA-SITE AMYLOID PRECURSOR COMPND 6 PROTEIN CLEAVING ENZYME 1,BETA-SITE APP CLEAVING ENZYME 1,MEMAPSIN-2, COMPND 7 MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 8 EC: 3.4.23.46; COMPND 9 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: BACE1, BACE, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, HYDROLASE- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.FUCHINO,Y.MITSUOKA,M.MASUI,N.KUROSE,S.YOSHIDA,K.KOMANO,T.YAMAMOTO, AUTHOR 2 M.OGAWA,C.UNEMURA,M.HOSONO,H.ITO,G.SAKAGUCHI,S.ANDO,S.OHNISHI, AUTHOR 3 Y.KIDO,T.FUKUSHIMA,H.MIYAJIMA,S.HIROYAMA,K.KOYABU,D.DHUYVETTER, AUTHOR 4 H.BORGHYS,H.GIJSEN,Y.YAMANO,Y.ISO,K.KUSAKABE REVDAT 4 22-NOV-23 5YGY 1 REMARK REVDAT 3 11-JUL-18 5YGY 1 JRNL REVDAT 2 30-MAY-18 5YGY 1 JRNL REVDAT 1 23-MAY-18 5YGY 0 JRNL AUTH K.FUCHINO,Y.MITSUOKA,M.MASUI,N.KUROSE,S.YOSHIDA,K.KOMANO, JRNL AUTH 2 T.YAMAMOTO,M.OGAWA,C.UNEMURA,M.HOSONO,H.ITO,G.SAKAGUCHI, JRNL AUTH 3 S.ANDO,S.OHNISHI,Y.KIDO,T.FUKUSHIMA,H.MIYAJIMA,S.HIROYAMA, JRNL AUTH 4 K.KOYABU,D.DHUYVETTER,H.BORGHYS,H.J.M.GIJSEN,Y.YAMANO,Y.ISO, JRNL AUTH 5 K.I.KUSAKABE JRNL TITL RATIONAL DESIGN OF NOVEL 1,3-OXAZINE BASED BETA-SECRETASE JRNL TITL 2 (BACE1) INHIBITORS: INCORPORATION OF A DOUBLE BOND TO REDUCE JRNL TITL 3 P-GP EFFLUX LEADING TO ROBUST A BETA REDUCTION IN THE BRAIN JRNL REF J. MED. CHEM. V. 61 5122 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29733614 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00002 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 21583 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2428 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1539 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.03000 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): 0.275 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.179 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3063 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4165 ; 1.494 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 379 ; 7.053 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;34.358 ;23.582 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 456 ;17.206 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;12.584 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 454 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2347 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5YGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24045 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.52900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1W50 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CITRATE TRIBASIC PH6.5, REMARK 280 0.2M AMMONIUM IODIDE, 20.5%(W/V) PEG5000MME, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 57.04167 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 114.08333 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 85.56250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 142.60417 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 28.52083 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.04167 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 114.08333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 142.60417 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 85.56250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 28.52083 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 TOTAL BURIED SURFACE AREA: 280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 -22 REMARK 465 SER A -21 REMARK 465 HIS A -20 REMARK 465 MET A -19 REMARK 465 LEU A -18 REMARK 465 PRO A -17 REMARK 465 ARG A -16 REMARK 465 GLU A -15 REMARK 465 THR A -14 REMARK 465 ASP A -13 REMARK 465 GLU A -12 REMARK 465 GLU A -11 REMARK 465 PRO A -10 REMARK 465 GLU A -9 REMARK 465 GLU A -8 REMARK 465 PRO A -7 REMARK 465 ALA A 157 REMARK 465 GLY A 158 REMARK 465 PHE A 159 REMARK 465 PRO A 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 GLU A 165 REMARK 465 VAL A 166 REMARK 465 LEU A 167 REMARK 465 ILE A 386 REMARK 465 PRO A 387 REMARK 465 GLN A 388 REMARK 465 THR A 389 REMARK 465 ASP A 390 REMARK 465 GLU A 391 REMARK 465 SER A 392 REMARK 465 THR A 393 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 ARG A -5 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 9 CE NZ REMARK 470 ARG A 64 NE CZ NH1 NH2 REMARK 470 LYS A 65 CE NZ REMARK 470 GLN A 73 CG CD OE1 NE2 REMARK 470 LYS A 142 CE NZ REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 LYS A 239 NZ REMARK 470 LYS A 246 CD CE NZ REMARK 470 LYS A 256 CG CD CE NZ REMARK 470 ILE A 279 CG1 CG2 CD1 REMARK 470 GLU A 310 CB CG CD OE1 OE2 REMARK 470 ASP A 311 CB CG OD1 OD2 REMARK 470 GLN A 316 CG CD OE1 NE2 REMARK 470 GLU A 364 CG CD OE1 OE2 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 A 149 CA - CB - CG ANGL. DEV. = 15.1 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 89 45.28 -104.01 REMARK 500 PHE A 108 -65.55 -102.24 REMARK 500 TRP A 197 -85.93 -140.14 REMARK 500 SER A 253 -9.04 -59.01 REMARK 500 ASP A 311 39.10 -78.78 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 IOD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0B6 A 509 DBREF 5YGY A -18 393 UNP P56817 BACE1_HUMAN 43 454 SEQADV 5YGY GLY A -22 UNP P56817 EXPRESSION TAG SEQADV 5YGY SER A -21 UNP P56817 EXPRESSION TAG SEQADV 5YGY HIS A -20 UNP P56817 EXPRESSION TAG SEQADV 5YGY MET A -19 UNP P56817 EXPRESSION TAG SEQRES 1 A 416 GLY SER HIS MET LEU PRO ARG GLU THR ASP GLU GLU PRO SEQRES 2 A 416 GLU GLU PRO GLY ARG ARG GLY SER PHE VAL GLU MET VAL SEQRES 3 A 416 ASP ASN LEU ARG GLY LYS SER GLY GLN GLY TYR TYR VAL SEQRES 4 A 416 GLU MET THR VAL GLY SER PRO PRO GLN THR LEU ASN ILE SEQRES 5 A 416 LEU VAL ASP THR GLY SER SER ASN PHE ALA VAL GLY ALA SEQRES 6 A 416 ALA PRO HIS PRO PHE LEU HIS ARG TYR TYR GLN ARG GLN SEQRES 7 A 416 LEU SER SER THR TYR ARG ASP LEU ARG LYS GLY VAL TYR SEQRES 8 A 416 VAL PRO TYR THR GLN GLY LYS TRP GLU GLY GLU LEU GLY SEQRES 9 A 416 THR ASP LEU VAL SER ILE PRO HIS GLY PRO ASN VAL THR SEQRES 10 A 416 VAL ARG ALA ASN ILE ALA ALA ILE THR GLU SER ASP LYS SEQRES 11 A 416 PHE PHE ILE ASN GLY SER ASN TRP GLU GLY ILE LEU GLY SEQRES 12 A 416 LEU ALA TYR ALA GLU ILE ALA ARG PRO ASP ASP SER LEU SEQRES 13 A 416 GLU PRO PHE PHE ASP SER LEU VAL LYS GLN THR HIS VAL SEQRES 14 A 416 PRO ASN LEU PHE SER LEU GLN LEU CYS GLY ALA GLY PHE SEQRES 15 A 416 PRO LEU ASN GLN SER GLU VAL LEU ALA SER VAL GLY GLY SEQRES 16 A 416 SER MET ILE ILE GLY GLY ILE ASP HIS SER LEU TYR THR SEQRES 17 A 416 GLY SER LEU TRP TYR THR PRO ILE ARG ARG GLU TRP TYR SEQRES 18 A 416 TYR GLU VAL ILE ILE VAL ARG VAL GLU ILE ASN GLY GLN SEQRES 19 A 416 ASP LEU LYS MET ASP CYS LYS GLU TYR ASN TYR ASP LYS SEQRES 20 A 416 SER ILE VAL ASP SER GLY THR THR ASN LEU ARG LEU PRO SEQRES 21 A 416 LYS LYS VAL PHE GLU ALA ALA VAL LYS SER ILE LYS ALA SEQRES 22 A 416 ALA SER SER THR GLU LYS PHE PRO ASP GLY PHE TRP LEU SEQRES 23 A 416 GLY GLU GLN LEU VAL CYS TRP GLN ALA GLY THR THR PRO SEQRES 24 A 416 TRP ASN ILE PHE PRO VAL ILE SER LEU TYR LEU MET GLY SEQRES 25 A 416 GLU VAL THR ASN GLN SER PHE ARG ILE THR ILE LEU PRO SEQRES 26 A 416 GLN GLN TYR LEU ARG PRO VAL GLU ASP VAL ALA THR SER SEQRES 27 A 416 GLN ASP ASP CYS TYR LYS PHE ALA ILE SER GLN SER SER SEQRES 28 A 416 THR GLY THR VAL MET GLY ALA VAL ILE MET GLU GLY PHE SEQRES 29 A 416 TYR VAL VAL PHE ASP ARG ALA ARG LYS ARG ILE GLY PHE SEQRES 30 A 416 ALA VAL SER ALA CYS HIS VAL HIS ASP GLU PHE ARG THR SEQRES 31 A 416 ALA ALA VAL GLU GLY PRO PHE VAL THR LEU ASP MET GLU SEQRES 32 A 416 ASP CYS GLY TYR ASN ILE PRO GLN THR ASP GLU SER THR HET IOD A 501 1 HET IOD A 502 1 HET IOD A 503 1 HET IOD A 504 1 HET IOD A 505 1 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET 0B6 A 509 28 HETNAM IOD IODIDE ION HETNAM GOL GLYCEROL HETNAM 0B6 ~{N}-[3-[(4~{S})-2-AZANYL-6-(FLUORANYLMETHYL)-4-METHYL- HETNAM 2 0B6 1,3-OXAZIN-4-YL]-4-FLUORANYL-PHENYL]-5-CYANO-PYRIDINE- HETNAM 3 0B6 2-CARBOXAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 IOD 5(I 1-) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 10 0B6 C19 H15 F2 N5 O2 FORMUL 11 HOH *199(H2 O) HELIX 1 AA1 PHE A -1 VAL A 3 5 5 HELIX 2 AA2 GLN A 53 SER A 57 5 5 HELIX 3 AA3 TYR A 123 ALA A 127 5 5 HELIX 4 AA4 PRO A 135 THR A 144 1 10 HELIX 5 AA5 ASP A 180 SER A 182 5 3 HELIX 6 AA6 ASP A 216 TYR A 222 5 7 HELIX 7 AA7 LYS A 238 SER A 252 1 15 HELIX 8 AA8 PRO A 258 LEU A 263 1 6 HELIX 9 AA9 PRO A 276 PHE A 280 5 5 HELIX 10 AB1 LEU A 301 TYR A 305 1 5 HELIX 11 AB2 GLY A 334 GLU A 339 1 6 HELIX 12 AB3 ARG A 347 ARG A 349 5 3 HELIX 13 AB4 ASP A 378 GLY A 383 5 6 SHEET 1 AA1 9 ARG A 61 PRO A 70 0 SHEET 2 AA1 9 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 SHEET 3 AA1 9 GLY A 13 VAL A 20 -1 N THR A 19 O SER A 86 SHEET 4 AA1 9 LEU A 6 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 5 AA1 9 SER A 169 ILE A 176 -1 O GLY A 172 N LEU A 6 SHEET 6 AA1 9 PHE A 150 LEU A 154 -1 N GLN A 153 O SER A 173 SHEET 7 AA1 9 PHE A 341 ASP A 346 -1 O VAL A 343 N LEU A 152 SHEET 8 AA1 9 ARG A 351 SER A 357 -1 O ALA A 355 N TYR A 342 SHEET 9 AA1 9 TYR A 184 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 AA213 ARG A 61 PRO A 70 0 SHEET 2 AA213 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 SHEET 3 AA213 VAL A 95 ASP A 106 -1 O VAL A 95 N VAL A 85 SHEET 4 AA213 PHE A 38 GLY A 41 1 N VAL A 40 O ILE A 102 SHEET 5 AA213 GLY A 117 GLY A 120 -1 O ILE A 118 N ALA A 39 SHEET 6 AA213 GLN A 25 ASP A 32 1 N LEU A 30 O LEU A 119 SHEET 7 AA213 GLY A 13 VAL A 20 -1 N TYR A 14 O VAL A 31 SHEET 8 AA213 LEU A 6 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 9 AA213 SER A 169 ILE A 176 -1 O GLY A 172 N LEU A 6 SHEET 10 AA213 PHE A 150 LEU A 154 -1 N GLN A 153 O SER A 173 SHEET 11 AA213 PHE A 341 ASP A 346 -1 O VAL A 343 N LEU A 152 SHEET 12 AA213 ARG A 351 SER A 357 -1 O ALA A 355 N TYR A 342 SHEET 13 AA213 TYR A 184 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 AA3 5 GLN A 211 ASP A 212 0 SHEET 2 AA3 5 ILE A 203 ILE A 208 -1 N ILE A 208 O GLN A 211 SHEET 3 AA3 5 ILE A 283 MET A 288 -1 O TYR A 286 N ARG A 205 SHEET 4 AA3 5 GLN A 294 ILE A 300 -1 O ILE A 300 N ILE A 283 SHEET 5 AA3 5 ALA A 369 VAL A 375 -1 O GLU A 371 N ARG A 297 SHEET 1 AA4 4 SER A 225 VAL A 227 0 SHEET 2 AA4 4 THR A 331 MET A 333 1 O MET A 333 N ILE A 226 SHEET 3 AA4 4 LEU A 234 PRO A 237 -1 N ARG A 235 O VAL A 332 SHEET 4 AA4 4 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 AA5 3 VAL A 268 TRP A 270 0 SHEET 2 AA5 3 ASP A 318 PHE A 322 -1 O TYR A 320 N VAL A 268 SHEET 3 AA5 3 LEU A 306 VAL A 309 -1 N VAL A 309 O CYS A 319 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.06 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.04 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.06 CISPEP 1 SER A 22 PRO A 23 0 -4.32 CISPEP 2 ARG A 128 PRO A 129 0 6.72 CISPEP 3 TYR A 222 ASP A 223 0 -3.06 CISPEP 4 GLY A 372 PRO A 373 0 -3.75 SITE 1 AC1 1 SER A 105 SITE 1 AC2 2 ARG A 349 HOH A 726 SITE 1 AC3 1 LYS A 107 SITE 1 AC4 1 ARG A 96 SITE 1 AC5 6 ARG A 50 TYR A 51 GLN A 53 SER A 187 SITE 2 AC5 6 GOL A 507 HOH A 626 SITE 1 AC6 6 HIS A 45 LEU A 48 TYR A 51 TRP A 189 SITE 2 AC6 6 PRO A 373 GOL A 506 SITE 1 AC7 5 SER A 10 GLY A 11 THR A 232 ARG A 307 SITE 2 AC7 5 PRO A 308 SITE 1 AC8 16 GLY A 11 GLN A 12 GLY A 13 LEU A 30 SITE 2 AC8 16 ASP A 32 GLY A 34 TYR A 71 PHE A 108 SITE 3 AC8 16 ASP A 228 SER A 229 GLY A 230 THR A 231 SITE 4 AC8 16 THR A 232 ALA A 335 HOH A 744 HOH A 749 CRYST1 102.149 102.149 171.125 90.00 90.00 120.00 P 61 2 2 12 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 0.009790 0.005652 0.000000 0.00000 SCALE2 0.000000 0.011304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005844 0.00000