HEADER HYDROLASE/IMMUNE SYSTEM 25-SEP-20 7D5B
TITLE BACE2 XAPERONE COMPLEX WITH N-{3-[(5R)-3-AMINO-2,5-DIMETHYL-1,1-DIOXO-
TITLE 2 5,6-DIHYDRO-2H-1LAMBDA6,2,4-THIADIAZIN-5-YL]-4-FLUOROPHENYL}-5-
TITLE 3 FLUOROPYRIDINE-2-CARBOXAMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-SECRETASE 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PROTEASE;
COMPND 5 SYNONYM: ASPARTIC-LIKE PROTEASE 56 KDA,ASPARTYL PROTEASE 1,ASP 1,
COMPND 6 BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2,BETA-SITE APP
COMPND 7 CLEAVING ENZYME 2,DOWN REGION ASPARTIC PROTEASE,DRAP,MEMAPSIN-1,
COMPND 8 MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1,THETA-SECRETASE;
COMPND 9 EC: 3.4.23.45;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 2;
COMPND 12 MOLECULE: XAPERONE;
COMPND 13 CHAIN: D;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_TAXID: 9606;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 8 ORGANISM_TAXID: 9606;
SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BACE1, HYDROLASE, HYDROLASE-IMMUNE SYSTEM COMPLEX
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 3 09-OCT-24 7D5B 1 REMARK
REVDAT 2 07-APR-21 7D5B 1 JRNL
REVDAT 1 31-MAR-21 7D5B 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. 1.31 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0155
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) : 1.31
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.70
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1
REMARK 3 NUMBER OF REFLECTIONS : 115272
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) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.222
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 6356
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) : 1.31
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.34
REMARK 3 REFLECTION IN BIN (WORKING SET) : 8598
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.32
REMARK 3 BIN R VALUE (WORKING SET) : 0.4120
REMARK 3 BIN FREE R VALUE SET COUNT : 443
REMARK 3 BIN FREE R VALUE : 0.4310
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3633
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 43
REMARK 3 SOLVENT ATOMS : 535
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.87
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.76000
REMARK 3 B22 (A**2) : -0.98000
REMARK 3 B33 (A**2) : 1.75000
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): 0.056
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3952 ; 0.013 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 3515 ; 0.000 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5406 ; 1.635 ; 1.957
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8161 ; 3.963 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 521 ; 7.113 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.476 ;24.065
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 601 ;10.954 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.979 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 601 ; 0.105 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4539 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 842 ; 0.010 ; 0.020
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 : 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 U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 7D5B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-20.
REMARK 100 THE DEPOSITION ID IS D_1300018777.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-OCT-18
REMARK 200 TEMPERATURE (KELVIN) : 100.000
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 121628
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310
REMARK 200 RESOLUTION RANGE LOW (A) : 61.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0
REMARK 200 DATA REDUNDANCY : 2.334
REMARK 200 R MERGE (I) : 0.04000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6
REMARK 200 DATA REDUNDANCY IN SHELL : 2.28
REMARK 200 R MERGE FOR SHELL (I) : 0.49300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.950
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5 % PEG1500, 0.01 M NA ACETATE PH
REMARK 280 4.5, 0.06 M NA CITRATE, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 293K
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 31.90350
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.20400
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.19800
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.20400
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.90350
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.19800
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2590 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D
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 PRO A 176
REMARK 465 VAL A 177
REMARK 465 ALA A 178
REMARK 465 GLY A 179
REMARK 465 SER A 180
REMARK 465 GLY A 181
REMARK 465 THR A 182
REMARK 465 SER A 286
REMARK 465 GLU A 287
REMARK 465 MET A 323
REMARK 465 GLY A 324
REMARK 465 ALA A 325
REMARK 465 GLY A 326
REMARK 465 LEU A 327
REMARK 465 ASN A 328
REMARK 465 TYR A 329
REMARK 465 ALA A 398
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 28 NE CZ NH1 NH2
REMARK 470 LYS A 42 NZ
REMARK 470 SER A 62 OG
REMARK 470 TYR A 63 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 ARG A 72 CZ NH1 NH2
REMARK 470 LYS A 86 CE NZ
REMARK 470 GLN A 89 CG CD OE1 NE2
REMARK 470 GLU A 122 CD OE1 OE2
REMARK 470 LEU A 126 CD1 CD2
REMARK 470 LYS A 130 NZ
REMARK 470 LYS A 198 CD CE NZ
REMARK 470 ASN A 227 CG OD1 ND2
REMARK 470 ARG A 263 CD NE CZ NH1 NH2
REMARK 470 GLU A 269 CG CD OE1 OE2
REMARK 470 ASN A 285 CG OD1 ND2
REMARK 470 GLU A 330 CG CD OE1 OE2
REMARK 470 THR A 340 OG1 CG2
REMARK 470 ASP A 390 CG OD1 OD2
REMARK 470 LYS D 202 NZ
REMARK 470 LYS D 224 CD CE NZ
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 ARG D 204 NE - CZ - NH1 ANGL. DEV. = 3.1 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 PHE A 124 -60.06 -99.14
REMARK 500 TRP A 210 -84.92 -141.73
REMARK 500 LYS A 237 149.63 170.37
REMARK 500 ASN A 341 -94.19 -118.03
REMARK 500 ALA D 251 165.36 177.54
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH D 580 DISTANCE = 5.95 ANGSTROMS
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 NA A 404 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 PRO A 39 O
REMARK 620 2 ARG A 72 O 137.2
REMARK 620 3 HOH A 572 O 72.0 119.5
REMARK 620 4 HOH A 804 O 103.4 98.1 129.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA D 303 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 605 O
REMARK 620 2 ILE D 192 O 122.8
REMARK 620 3 SER D 257 OG 67.4 72.8
REMARK 620 N 1 2
DBREF 7D5B A 13 398 UNP Q9Y5Z0 BACE2_HUMAN 75 460
DBREF 7D5B D 160 271 PDB 7D5B 7D5B 160 271
SEQRES 1 A 386 ALA ASN PHE LEU ALA MET VAL ASP ASN LEU GLN GLY ASP
SEQRES 2 A 386 SER GLY ARG GLY TYR TYR LEU GLU MET LEU ILE GLY THR
SEQRES 3 A 386 PRO PRO GLN LYS LEU GLN ILE LEU VAL ASP THR GLY SER
SEQRES 4 A 386 SER ASN PHE ALA VAL ALA GLY THR PRO HIS SER TYR ILE
SEQRES 5 A 386 ASP THR TYR PHE ASP THR GLU ARG SER SER THR TYR ARG
SEQRES 6 A 386 SER LYS GLY PHE ASP VAL THR VAL LYS TYR THR GLN GLY
SEQRES 7 A 386 SER TRP THR GLY PHE VAL GLY GLU ASP LEU VAL THR ILE
SEQRES 8 A 386 PRO LYS GLY PHE ASN THR SER PHE LEU VAL ASN ILE ALA
SEQRES 9 A 386 THR ILE PHE GLU SER GLU ASN PHE PHE LEU PRO GLY ILE
SEQRES 10 A 386 LYS TRP ASN GLY ILE LEU GLY LEU ALA TYR ALA THR LEU
SEQRES 11 A 386 ALA LYS PRO SER SER SER LEU GLU THR PHE PHE ASP SER
SEQRES 12 A 386 LEU VAL THR GLN ALA ASN ILE PRO ASN VAL PHE SER MET
SEQRES 13 A 386 GLN MET CYS GLY ALA GLY LEU PRO VAL ALA GLY SER GLY
SEQRES 14 A 386 THR ASN GLY GLY SER LEU VAL LEU GLY GLY ILE GLU PRO
SEQRES 15 A 386 SER LEU TYR LYS GLY ASP ILE TRP TYR THR PRO ILE LYS
SEQRES 16 A 386 GLU GLU TRP TYR TYR GLN ILE GLU ILE LEU LYS LEU GLU
SEQRES 17 A 386 ILE GLY GLY GLN SER LEU ASN LEU ASP CYS ARG GLU TYR
SEQRES 18 A 386 ASN ALA ASP LYS ALA ILE VAL ASP SER GLY THR THR LEU
SEQRES 19 A 386 LEU ARG LEU PRO GLN LYS VAL PHE ASP ALA VAL VAL GLU
SEQRES 20 A 386 ALA VAL ALA ARG ALA SER LEU ILE PRO GLU PHE SER ASP
SEQRES 21 A 386 GLY PHE TRP THR GLY SER GLN LEU ALA CYS TRP THR ASN
SEQRES 22 A 386 SER GLU THR PRO TRP SER TYR PHE PRO LYS ILE SER ILE
SEQRES 23 A 386 TYR LEU ARG ASP GLU ASN SER SER ARG SER PHE ARG ILE
SEQRES 24 A 386 THR ILE LEU PRO GLN LEU TYR ILE GLN PRO MET MET GLY
SEQRES 25 A 386 ALA GLY LEU ASN TYR GLU CYS TYR ARG PHE GLY ILE SER
SEQRES 26 A 386 PRO SER THR ASN ALA LEU VAL ILE GLY ALA THR VAL MET
SEQRES 27 A 386 GLU GLY PHE TYR VAL ILE PHE ASP ARG ALA GLN LYS ARG
SEQRES 28 A 386 VAL GLY PHE ALA ALA SER PRO CYS ALA GLU ILE ALA GLY
SEQRES 29 A 386 ALA ALA VAL SER GLU ILE SER GLY PRO PHE SER THR GLU
SEQRES 30 A 386 ASP VAL ALA SER ASN CYS VAL PRO ALA
SEQRES 1 D 112 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN
SEQRES 2 D 112 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY
SEQRES 3 D 112 PHE THR PHE SER SER ALA ILE MET THR TRP VAL ARG GLN
SEQRES 4 D 112 ALA PRO GLY LYS GLY ARG GLU TRP VAL SER THR ILE GLY
SEQRES 5 D 112 SER ASP GLY SER ILE THR THR TYR ALA ASP SER VAL LYS
SEQRES 6 D 112 GLY ARG PHE THR ILE SER ARG ASP ASN ALA ARG ASN THR
SEQRES 7 D 112 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR
SEQRES 8 D 112 ALA VAL TYR TYR CYS THR SER ALA GLY ARG ARG GLY PRO
SEQRES 9 D 112 GLY THR GLN VAL THR VAL SER SER
HET 66F A 401 28
HET CL A 402 1
HET EDO A 403 4
HET NA A 404 1
HET EDO D 301 4
HET EDO D 302 4
HET NA D 303 1
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
HETNAM CL CHLORIDE ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM NA SODIUM ION
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 66F C17 H17 F2 N5 O3 S
FORMUL 4 CL CL 1-
FORMUL 5 EDO 3(C2 H6 O2)
FORMUL 6 NA 2(NA 1+)
FORMUL 10 HOH *535(H2 O)
HELIX 1 AA1 PHE A 15 VAL A 19 5 5
HELIX 2 AA2 ASP A 69 SER A 73 5 5
HELIX 3 AA3 TYR A 139 ALA A 143 5 5
HELIX 4 AA4 THR A 151 ASN A 161 1 11
HELIX 5 AA5 GLU A 193 TYR A 197 5 5
HELIX 6 AA6 ASP A 229 ASN A 234 5 6
HELIX 7 AA7 GLN A 251 SER A 265 1 15
HELIX 8 AA8 SER A 271 THR A 276 1 6
HELIX 9 AA9 PRO A 289 PHE A 293 5 5
HELIX 10 AB1 PRO A 315 LEU A 317 5 3
HELIX 11 AB2 GLY A 346 GLU A 351 1 6
HELIX 12 AB3 THR D 187 ALA D 191 5 5
HELIX 13 AB4 ASP D 221 LYS D 224 5 4
HELIX 14 AB5 ASN D 233 ARG D 235 5 3
HELIX 15 AB6 LYS D 246 THR D 250 5 5
SHEET 1 AA1 8 LEU A 22 ASP A 25 0
SHEET 2 AA1 8 GLY A 29 ILE A 36 -1 O TYR A 31 N GLN A 23
SHEET 3 AA1 8 GLN A 41 ASP A 48 -1 O LEU A 43 N MET A 34
SHEET 4 AA1 8 GLY A 133 GLY A 136 1 O LEU A 135 N LEU A 46
SHEET 5 AA1 8 PHE A 54 ALA A 57 -1 N ALA A 55 O ILE A 134
SHEET 6 AA1 8 PHE A 111 GLU A 122 1 O ILE A 118 N VAL A 56
SHEET 7 AA1 8 GLY A 90 THR A 102 -1 N SER A 91 O GLU A 122
SHEET 8 AA1 8 ARG A 77 TYR A 87 -1 N TYR A 87 O GLY A 90
SHEET 1 AA2 4 LEU A 22 ASP A 25 0
SHEET 2 AA2 4 GLY A 29 ILE A 36 -1 O TYR A 31 N GLN A 23
SHEET 3 AA2 4 GLY A 90 THR A 102 -1 O THR A 102 N LEU A 35
SHEET 4 AA2 4 ARG A 77 TYR A 87 -1 N TYR A 87 O GLY A 90
SHEET 1 AA3 6 GLY A 185 LEU A 189 0
SHEET 2 AA3 6 PHE A 166 MET A 170 -1 N SER A 167 O VAL A 188
SHEET 3 AA3 6 PHE A 353 ASP A 358 -1 O PHE A 357 N PHE A 166
SHEET 4 AA3 6 ARG A 363 ALA A 368 -1 O ALA A 367 N TYR A 354
SHEET 5 AA3 6 TRP A 202 GLU A 208 -1 N THR A 204 O VAL A 364
SHEET 6 AA3 6 GLN A 213 ILE A 214 -1 O GLN A 213 N LYS A 207
SHEET 1 AA4 5 GLN A 224 SER A 225 0
SHEET 2 AA4 5 ILE A 216 ILE A 221 -1 N ILE A 221 O GLN A 224
SHEET 3 AA4 5 ILE A 296 ARG A 301 -1 O SER A 297 N GLU A 220
SHEET 4 AA4 5 ARG A 307 ILE A 313 -1 O ILE A 311 N ILE A 298
SHEET 5 AA4 5 SER A 380 SER A 387 -1 O GLU A 381 N THR A 312
SHEET 1 AA5 2 ALA A 238 VAL A 240 0
SHEET 2 AA5 2 LEU A 343 ILE A 345 1 O ILE A 345 N ILE A 239
SHEET 1 AA6 2 LEU A 247 PRO A 250 0
SHEET 2 AA6 2 ILE A 336 SER A 339 1 O SER A 337 N LEU A 249
SHEET 1 AA7 3 ALA A 281 CYS A 282 0
SHEET 2 AA7 3 CYS A 331 PHE A 334 -1 O TYR A 332 N ALA A 281
SHEET 3 AA7 3 ILE A 319 PRO A 321 -1 N GLN A 320 O ARG A 333
SHEET 1 AA8 2 GLU A 373 ILE A 374 0
SHEET 2 AA8 2 ALA A 377 ALA A 378 -1 O ALA A 377 N ILE A 374
SHEET 1 AA9 4 GLN D 162 SER D 166 0
SHEET 2 AA9 4 LEU D 177 SER D 184 -1 O SER D 184 N GLN D 162
SHEET 3 AA9 4 THR D 237 MET D 242 -1 O MET D 242 N LEU D 177
SHEET 4 AA9 4 PHE D 227 ASP D 232 -1 N SER D 230 O TYR D 239
SHEET 1 AB1 6 GLY D 169 VAL D 171 0
SHEET 2 AB1 6 THR D 265 VAL D 269 1 O THR D 268 N GLY D 169
SHEET 3 AB1 6 ALA D 251 SER D 257 -1 N TYR D 253 O THR D 265
SHEET 4 AB1 6 MET D 193 GLN D 198 -1 N VAL D 196 O TYR D 254
SHEET 5 AB1 6 GLU D 205 ILE D 210 -1 O SER D 208 N TRP D 195
SHEET 6 AB1 6 THR D 217 TYR D 219 -1 O THR D 218 N THR D 209
SHEET 1 AB2 4 GLY D 169 VAL D 171 0
SHEET 2 AB2 4 THR D 265 VAL D 269 1 O THR D 268 N GLY D 169
SHEET 3 AB2 4 ALA D 251 SER D 257 -1 N TYR D 253 O THR D 265
SHEET 4 AB2 4 ARG D 260 ARG D 261 -1 O ARG D 260 N SER D 257
SSBOND 1 CYS A 171 CYS A 371 1555 1555 2.13
SSBOND 2 CYS A 230 CYS A 395 1555 1555 2.07
SSBOND 3 CYS A 282 CYS A 331 1555 1555 2.04
LINK O PRO A 39 NA NA A 404 1555 1555 2.35
LINK O ARG A 72 NA NA A 404 1555 1555 2.66
LINK NA NA A 404 O HOH A 572 1555 1555 2.29
LINK NA NA A 404 O HOH A 804 1555 1555 2.55
LINK O HOH A 605 NA NA D 303 1555 1555 2.88
LINK O ILE D 192 NA NA D 303 1555 1555 2.68
LINK OG SER D 257 NA NA D 303 1555 1555 2.20
CISPEP 1 THR A 38 PRO A 39 0 -9.02
CISPEP 2 LYS A 144 PRO A 145 0 3.51
CISPEP 3 GLY A 384 PRO A 385 0 -1.24
CRYST1 63.807 74.396 110.408 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 0.015672 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013442 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009057 0.00000