HEADER HYDROLASE 17-SEP-20 7D2V
TITLE CRYSTAL STRUCTURE OF BACE1 IN COMPLEX WITH N-{3-[(5R)-3-AMINO-2,5-
TITLE 2 DIMETHYL-1,1-DIOXO-5,6-DIHYDRO-2H-1LAMBDA6,2,4-THIADIAZIN-5-YL]-4-
TITLE 3 FLUOROPHENYL}-5-FLUOROPYRIDINE-2-CARBOXAMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-SECRETASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ASPARTYL PROTEASE 2,ASP 2,BETA-SITE AMYLOID PRECURSOR
COMPND 5 PROTEIN CLEAVING ENZYME 1,BETA-SITE APP CLEAVING ENZYME 1,MEMAPSIN-2,
COMPND 6 MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2;
COMPND 7 EC: 3.4.23.46;
COMPND 8 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 BACE1, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.FUJIMOTO,S.YOSHIDA,G.TADANO,N.ASADA,K.FUCHINO,S.SUZUKI,E.MATSUOKA,
AUTHOR 2 T.YAMAMOTO,S.YAMAMOTO,S.ANDO,N.KANEGAWA,Y.TONOMURA,H.ITO,D.MOECHARS,
AUTHOR 3 F.J.R.ROMBOUTS,H.J.M.GIJSEN,K.I.KUSAKABE
REVDAT 4 16-OCT-24 7D2V 1 REMARK
REVDAT 3 29-NOV-23 7D2V 1 REMARK
REVDAT 2 07-APR-21 7D2V 1 JRNL
REVDAT 1 31-MAR-21 7D2V 0
JRNL AUTH K.FUJIMOTO,S.YOSHIDA,G.TADANO,N.ASADA,K.FUCHINO,S.SUZUKI,
JRNL AUTH 2 E.MATSUOKA,T.YAMAMOTO,S.YAMAMOTO,S.ANDO,N.KANEGAWA,
JRNL AUTH 3 Y.TONOMURA,H.ITO,D.MOECHARS,F.J.R.ROMBOUTS,H.J.M.GIJSEN,
JRNL AUTH 4 K.I.KUSAKABE
JRNL TITL STRUCTURE-BASED APPROACHES TO IMPROVING SELECTIVITY THROUGH
JRNL TITL 2 UTILIZING EXPLICIT WATER MOLECULES: DISCOVERY OF SELECTIVE
JRNL TITL 3 BETA-SECRETASE (BACE1) INHIBITORS OVER BACE2.
JRNL REF J.MED.CHEM. V. 64 3075 2021
JRNL REFN ISSN 0022-2623
JRNL PMID 33719429
JRNL DOI 10.1021/ACS.JMEDCHEM.0C01858
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 28330
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) : 0.210
REMARK 3 R VALUE (WORKING SET) : 0.206
REMARK 3 FREE R VALUE : 0.245
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3154
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) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2013
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.05
REMARK 3 BIN R VALUE (WORKING SET) : 0.2470
REMARK 3 BIN FREE R VALUE SET COUNT : 198
REMARK 3 BIN FREE R VALUE : 0.2860
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2935
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 43
REMARK 3 SOLVENT ATOMS : 231
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.19
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.13000
REMARK 3 B22 (A**2) : -0.13000
REMARK 3 B33 (A**2) : 0.41000
REMARK 3 B12 (A**2) : -0.13000
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): 0.205
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.505
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3053 ; 0.008 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4158 ; 1.233 ; 1.958
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 6.483 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;34.080 ;23.433
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 459 ;15.609 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;14.593 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 453 ; 0.082 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2352 ; 0.005 ; 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 : 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 USED IF PRESENT IN
REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 7D2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-SEP-20.
REMARK 100 THE DEPOSITION ID IS D_1300018635.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-NOV-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
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 FR-E+ SUPERBRIGHT
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31499
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 10.50
REMARK 200 R MERGE (I) : 0.09800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.53800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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 (%): 56.07
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE TRIBASIC PH 6.5,
REMARK 280 0.2 M AMMONIUM IODIDE, 19.5% W/V PEG 5000MME, 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 56.86367
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 113.72733
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 85.29550
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 142.15917
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 28.43183
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 56.86367
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 113.72733
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 142.15917
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 85.29550
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 28.43183
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 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 GLY A -6
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 ALA A 168
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 CG CD CE NZ
REMARK 470 GLN A 73 CB 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 CE NZ
REMARK 470 LYS A 246 CG CD CE NZ
REMARK 470 LYS A 256 CE NZ
REMARK 470 GLN A 271 CG CD OE1 NE2
REMARK 470 THR A 274 OG1 CG2
REMARK 470 GLU A 310 CG CD OE1 OE2
REMARK 470 ASP A 311 CG OD1 OD2
REMARK 470 SER A 315 CB OG
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: 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 812 O HOH A 812 10664 2.02
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 A -1 62.09 -150.22
REMARK 500 HIS A 89 45.93 -101.51
REMARK 500 PHE A 108 -66.95 -102.65
REMARK 500 TRP A 197 -86.37 -137.27
REMARK 500 ASN A 293 13.30 59.64
REMARK 500
REMARK 500 REMARK: NULL
DBREF 7D2V A -18 393 UNP P56817 BACE1_HUMAN 43 454
SEQADV 7D2V GLY A -22 UNP P56817 EXPRESSION TAG
SEQADV 7D2V SER A -21 UNP P56817 EXPRESSION TAG
SEQADV 7D2V HIS A -20 UNP P56817 EXPRESSION TAG
SEQADV 7D2V 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 GOL A 504 6
HET GOL A 505 6
HET 66F A 506 28
HETNAM IOD IODIDE ION
HETNAM GOL GLYCEROL
HETNAM 66F N-{3-[(5R)-3-AMINO-2,5-DIMETHYL-1,1-DIOXIDO-5,6-
HETNAM 2 66F DIHYDRO-2H-1,2,4-THIADIAZIN-5-YL]-4-FLUOROPHENYL}-5-
HETNAM 3 66F FLUOROPYRIDINE-2-CARBOXAMIDE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 IOD 3(I 1-)
FORMUL 5 GOL 2(C3 H8 O3)
FORMUL 7 66F C17 H17 F2 N5 O3 S
FORMUL 8 HOH *231(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 220 5 5
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 MET A 379 GLY A 383 5 5
SHEET 1 AA1 9 ARG A 61 TYR A 71 0
SHEET 2 AA1 9 GLY A 74 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 VAL A 170 ILE A 176 -1 O GLY A 172 N LEU A 6
SHEET 6 AA1 9 PHE A 150 CYS A 155 -1 N CYS A 155 O GLY A 171
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 TYR A 71 0
SHEET 2 AA213 GLY A 74 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 VAL A 170 ILE A 176 -1 O GLY A 172 N LEU A 6
SHEET 10 AA213 PHE A 150 CYS A 155 -1 N CYS A 155 O GLY A 171
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 2.07
SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.05
SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.04
CISPEP 1 SER A 22 PRO A 23 0 -3.66
CISPEP 2 ARG A 128 PRO A 129 0 5.01
CISPEP 3 TYR A 222 ASP A 223 0 1.82
CISPEP 4 GLY A 372 PRO A 373 0 -4.83
CRYST1 102.720 102.720 170.591 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 0.009735 0.005621 0.000000 0.00000
SCALE2 0.000000 0.011241 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005862 0.00000