HEADER HYDROLASE 23-JAN-13 3ZKG TITLE BACE2 MUTANT APO STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EXTRACELLULAR, RESIDUES 75-460; COMPND 5 SYNONYM: ASPARTIC-LIKE PROTEASE 56 KDA, ASPARTYL PROTEASE 1, ASP1, COMPND 6 ASP 1, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2, BETA- COMPND 7 SITE APP CLEAVING ENZYME 2, DOWN REGION ASPARTIC PROTEASE, DRAP, COMPND 8 MEMAPSIN-1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1, THETA-SECRETASE, COMPND 9 BACE2; COMPND 10 EC: 3.4.23.45; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,A.KUGLSTATTER,J.BENZ,M.STIHLE,A.RUF REVDAT 3 20-DEC-23 3ZKG 1 REMARK REVDAT 2 05-JUN-13 3ZKG 1 JRNL REVDAT 1 29-MAY-13 3ZKG 0 JRNL AUTH D.W.BANNER,B.GSELL,J.BENZ,J.BERTSCHINGER,D.BURGER,S.BRACK, JRNL AUTH 2 S.CUPPULERI,M.DEBULPAEP,A.GAST,D.GRABULOVSKI,M.HENNIG, JRNL AUTH 3 H.HILPERT,W.HUBER,A.KUGLSTATTER,E.KUSZNIR,T.LAEREMANS, JRNL AUTH 4 H.MATILE,C.MISCENIC,A.RUFER,D.SCHLATTER,J.STEYEART,M.STIHLE, JRNL AUTH 5 R.THOMA,M.WEBER,A.RUF JRNL TITL MAPPING THE CONFORMATIONAL SPACE ACCESSIBLE TO BACE2 USING JRNL TITL 2 SURFACE MUTANTS AND CO-CRYSTALS WITH FAB-FRAGMENTS, JRNL TITL 3 FYNOMERS, AND XAPERONES JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1124 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23695257 JRNL DOI 10.1107/S0907444913006574 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 58113 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3101 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) : 4217 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 226 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5600 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 302 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.73000 REMARK 3 B22 (A**2) : 1.18000 REMARK 3 B33 (A**2) : 0.61000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.517 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.880 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5794 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5382 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7878 ; 1.381 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12381 ; 0.773 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 720 ; 6.648 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;36.990 ;24.228 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 909 ;15.047 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.640 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 874 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6558 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1342 ; 0.001 ; 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 : 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 ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 3ZKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1290055535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61792 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 32.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.570 REMARK 200 R MERGE (I) : 0.01000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1000 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) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.61 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2EWY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH8, 25% PEG3350, PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 44.23300 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ALA A 13 REMARK 465 LEU A 175 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 PRO A 268 REMARK 465 ALA A 269 REMARK 465 THR A 284 REMARK 465 ASN A 285 REMARK 465 SER A 286 REMARK 465 GLU A 287 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 465 ALA B 13 REMARK 465 ASN B 14 REMARK 465 PHE B 15 REMARK 465 GLY B 174 REMARK 465 LEU B 175 REMARK 465 PRO B 176 REMARK 465 VAL B 177 REMARK 465 ALA B 178 REMARK 465 GLY B 179 REMARK 465 SER B 180 REMARK 465 GLY B 181 REMARK 465 THR B 182 REMARK 465 LEU B 266 REMARK 465 ILE B 267 REMARK 465 PRO B 268 REMARK 465 ALA B 269 REMARK 465 PHE B 270 REMARK 465 THR B 284 REMARK 465 ASN B 285 REMARK 465 SER B 286 REMARK 465 GLU B 287 REMARK 465 ALA B 325 REMARK 465 GLY B 326 REMARK 465 LEU B 327 REMARK 465 ASN B 328 REMARK 465 TYR B 329 REMARK 465 ALA B 398 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 B 2032 O HOH B 2080 2.19 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 210 -82.89 -145.81 REMARK 500 ASP A 236 -71.11 75.32 REMARK 500 SER A 265 -108.63 -102.65 REMARK 500 LEU A 266 44.73 120.69 REMARK 500 ALA B 138 -164.09 -78.99 REMARK 500 TRP B 210 -83.41 -140.53 REMARK 500 LYS B 218 136.16 -178.96 REMARK 500 ASN B 227 12.40 53.42 REMARK 500 ARG B 263 3.15 -69.22 REMARK 500 ASP B 272 -69.02 79.27 REMARK 500 PRO B 315 -39.79 -36.17 REMARK 500 MET B 323 -160.60 -111.60 REMARK 500 ASN B 341 -55.02 -166.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B3P A 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZKI RELATED DB: PDB REMARK 900 BACE2 MUTANT STRUCTURE WITH LIGAND REMARK 900 RELATED ID: 3ZKM RELATED DB: PDB REMARK 900 BACE2 FAB COMPLEX REMARK 900 RELATED ID: 3ZKN RELATED DB: PDB REMARK 900 BACE2 FAB INHIBITOR COMPLEX REMARK 900 RELATED ID: 3ZKQ RELATED DB: PDB REMARK 900 BACE2 XAPERONE COMPLEX REMARK 900 RELATED ID: 3ZKS RELATED DB: PDB REMARK 900 BACE2 XAPERONE COMPLEX WITH INHIBITOR REMARK 900 RELATED ID: 3ZKX RELATED DB: PDB REMARK 900 TERNARY BACE2 XAPERONE COMPLEX REMARK 900 RELATED ID: 3ZL7 RELATED DB: PDB REMARK 900 BACE2 FYNOMER COMPLEX REMARK 900 RELATED ID: 3ZOV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH CHEMICAL LIGAND REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS REMARK 999 NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. THE MUTATION REMARK 999 HERE IS E269A IN THE PDB FILE AND E331A IN THE DATA BANK REMARK 999 SEQUENCE. DBREF 3ZKG A 13 398 UNP Q9Y5Z0 BACE2_HUMAN 75 460 DBREF 3ZKG B 13 398 UNP Q9Y5Z0 BACE2_HUMAN 75 460 SEQADV 3ZKG ALA A 269 UNP Q9Y5Z0 GLU 331 ENGINEERED MUTATION SEQADV 3ZKG ALA B 269 UNP Q9Y5Z0 GLU 331 ENGINEERED MUTATION 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 ALA 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 B 386 ALA ASN PHE LEU ALA MET VAL ASP ASN LEU GLN GLY ASP SEQRES 2 B 386 SER GLY ARG GLY TYR TYR LEU GLU MET LEU ILE GLY THR SEQRES 3 B 386 PRO PRO GLN LYS LEU GLN ILE LEU VAL ASP THR GLY SER SEQRES 4 B 386 SER ASN PHE ALA VAL ALA GLY THR PRO HIS SER TYR ILE SEQRES 5 B 386 ASP THR TYR PHE ASP THR GLU ARG SER SER THR TYR ARG SEQRES 6 B 386 SER LYS GLY PHE ASP VAL THR VAL LYS TYR THR GLN GLY SEQRES 7 B 386 SER TRP THR GLY PHE VAL GLY GLU ASP LEU VAL THR ILE SEQRES 8 B 386 PRO LYS GLY PHE ASN THR SER PHE LEU VAL ASN ILE ALA SEQRES 9 B 386 THR ILE PHE GLU SER GLU ASN PHE PHE LEU PRO GLY ILE SEQRES 10 B 386 LYS TRP ASN GLY ILE LEU GLY LEU ALA TYR ALA THR LEU SEQRES 11 B 386 ALA LYS PRO SER SER SER LEU GLU THR PHE PHE ASP SER SEQRES 12 B 386 LEU VAL THR GLN ALA ASN ILE PRO ASN VAL PHE SER MET SEQRES 13 B 386 GLN MET CYS GLY ALA GLY LEU PRO VAL ALA GLY SER GLY SEQRES 14 B 386 THR ASN GLY GLY SER LEU VAL LEU GLY GLY ILE GLU PRO SEQRES 15 B 386 SER LEU TYR LYS GLY ASP ILE TRP TYR THR PRO ILE LYS SEQRES 16 B 386 GLU GLU TRP TYR TYR GLN ILE GLU ILE LEU LYS LEU GLU SEQRES 17 B 386 ILE GLY GLY GLN SER LEU ASN LEU ASP CYS ARG GLU TYR SEQRES 18 B 386 ASN ALA ASP LYS ALA ILE VAL ASP SER GLY THR THR LEU SEQRES 19 B 386 LEU ARG LEU PRO GLN LYS VAL PHE ASP ALA VAL VAL GLU SEQRES 20 B 386 ALA VAL ALA ARG ALA SER LEU ILE PRO ALA PHE SER ASP SEQRES 21 B 386 GLY PHE TRP THR GLY SER GLN LEU ALA CYS TRP THR ASN SEQRES 22 B 386 SER GLU THR PRO TRP SER TYR PHE PRO LYS ILE SER ILE SEQRES 23 B 386 TYR LEU ARG ASP GLU ASN SER SER ARG SER PHE ARG ILE SEQRES 24 B 386 THR ILE LEU PRO GLN LEU TYR ILE GLN PRO MET MET GLY SEQRES 25 B 386 ALA GLY LEU ASN TYR GLU CYS TYR ARG PHE GLY ILE SER SEQRES 26 B 386 PRO SER THR ASN ALA LEU VAL ILE GLY ALA THR VAL MET SEQRES 27 B 386 GLU GLY PHE TYR VAL ILE PHE ASP ARG ALA GLN LYS ARG SEQRES 28 B 386 VAL GLY PHE ALA ALA SER PRO CYS ALA GLU ILE ALA GLY SEQRES 29 B 386 ALA ALA VAL SER GLU ILE SER GLY PRO PHE SER THR GLU SEQRES 30 B 386 ASP VAL ALA SER ASN CYS VAL PRO ALA HET B3P A1000 19 HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL FORMUL 3 B3P C11 H26 N2 O6 FORMUL 4 HOH *302(H2 O) HELIX 1 1 ASN A 14 MET A 18 5 5 HELIX 2 2 ASP A 69 SER A 73 5 5 HELIX 3 3 TYR A 139 ALA A 143 5 5 HELIX 4 4 THR A 151 ASN A 161 1 11 HELIX 5 5 GLU A 193 TYR A 197 5 5 HELIX 6 6 ASP A 229 ALA A 235 5 7 HELIX 7 7 GLN A 251 SER A 265 1 15 HELIX 8 8 SER A 271 THR A 276 1 6 HELIX 9 9 THR A 288 PHE A 293 5 6 HELIX 10 10 LEU A 314 TYR A 318 1 5 HELIX 11 11 GLY A 346 GLU A 351 1 6 HELIX 12 12 ASP B 69 SER B 73 5 5 HELIX 13 13 TYR B 139 ALA B 143 5 5 HELIX 14 14 THR B 151 ASN B 161 1 11 HELIX 15 15 GLU B 193 TYR B 197 5 5 HELIX 16 16 ASP B 229 TYR B 233 5 5 HELIX 17 17 GLN B 251 ARG B 263 1 13 HELIX 18 18 THR B 288 PHE B 293 5 6 HELIX 19 19 LEU B 314 TYR B 318 1 5 HELIX 20 20 GLY B 346 GLU B 351 1 6 SHEET 1 AA 3 ARG A 77 LYS A 86 0 SHEET 2 AA 3 SER A 91 ILE A 103 -1 O TRP A 92 N VAL A 85 SHEET 3 AA 3 GLY A 29 ILE A 36 -1 O LEU A 35 N THR A 102 SHEET 1 AB 2 ARG A 77 LYS A 86 0 SHEET 2 AB 2 SER A 91 ILE A 103 -1 O TRP A 92 N VAL A 85 SHEET 1 AC 5 GLN A 224 SER A 225 0 SHEET 2 AC 5 ILE A 216 ILE A 221 -1 O ILE A 221 N GLN A 224 SHEET 3 AC 5 ILE A 296 ARG A 301 -1 O SER A 297 N GLU A 220 SHEET 4 AC 5 ARG A 307 ILE A 313 -1 O PHE A 309 N LEU A 300 SHEET 5 AC 5 SER A 380 SER A 387 -1 O GLU A 381 N THR A 312 SHEET 1 AD 2 LYS A 237 VAL A 240 0 SHEET 2 AD 2 ALA A 342 ILE A 345 1 O LEU A 343 N ILE A 239 SHEET 1 AE 2 LEU A 247 PRO A 250 0 SHEET 2 AE 2 ILE A 336 SER A 339 1 O SER A 337 N LEU A 249 SHEET 1 AF 6 ILE A 319 PRO A 321 0 SHEET 2 AF 6 CYS A 331 PHE A 334 -1 O ARG A 333 N GLN A 320 SHEET 3 AF 6 GLN A 279 CYS A 282 -1 O ALA A 281 N TYR A 332 SHEET 4 AF 6 GLN B 279 CYS B 282 -1 O LEU B 280 N LEU A 280 SHEET 5 AF 6 CYS B 331 PHE B 334 -1 O TYR B 332 N ALA B 281 SHEET 6 AF 6 ILE B 319 PRO B 321 -1 O GLN B 320 N ARG B 333 SHEET 1 AG 2 GLU A 373 ILE A 374 0 SHEET 2 AG 2 ALA A 377 ALA A 378 -1 O ALA A 377 N ILE A 374 SHEET 1 BA 7 LEU B 22 ASP B 25 0 SHEET 2 BA 7 GLY B 29 ILE B 36 -1 O GLY B 29 N ASP B 25 SHEET 3 BA 7 GLN B 41 ASP B 48 -1 O GLN B 41 N ILE B 36 SHEET 4 BA 7 GLY B 133 GLY B 136 1 O GLY B 133 N LEU B 46 SHEET 5 BA 7 PHE B 54 ALA B 57 -1 O ALA B 55 N ILE B 134 SHEET 6 BA 7 PHE B 111 GLU B 122 1 O ALA B 116 N VAL B 56 SHEET 7 BA 7 SER B 91 THR B 102 -1 O SER B 91 N GLU B 122 SHEET 1 BB 2 LEU B 22 ASP B 25 0 SHEET 2 BB 2 GLY B 29 ILE B 36 -1 O GLY B 29 N ASP B 25 SHEET 1 BC 5 GLY B 185 LEU B 189 0 SHEET 2 BC 5 VAL B 165 MET B 170 -1 O SER B 167 N VAL B 188 SHEET 3 BC 5 PHE B 353 ASP B 358 -1 O PHE B 353 N MET B 170 SHEET 4 BC 5 ARG B 363 ALA B 368 -1 O ARG B 363 N ASP B 358 SHEET 5 BC 5 LYS B 198 PRO B 205 -1 O LYS B 198 N ALA B 368 SHEET 1 BD 3 GLN B 213 ILE B 214 0 SHEET 2 BD 3 LYS B 237 VAL B 240 -1 O ALA B 238 N ILE B 214 SHEET 3 BD 3 ALA B 342 ILE B 345 1 O LEU B 343 N ILE B 239 SHEET 1 BE 4 ILE B 216 ILE B 221 0 SHEET 2 BE 4 ILE B 296 ARG B 301 -1 O SER B 297 N GLU B 220 SHEET 3 BE 4 ARG B 307 ILE B 313 -1 O PHE B 309 N LEU B 300 SHEET 4 BE 4 SER B 380 SER B 387 -1 O GLU B 381 N THR B 312 SHEET 1 BF 2 LEU B 247 PRO B 250 0 SHEET 2 BF 2 ILE B 336 SER B 339 1 O SER B 337 N LEU B 249 SHEET 1 BG 2 GLU B 373 ILE B 374 0 SHEET 2 BG 2 ALA B 377 ALA B 378 -1 O ALA B 377 N ILE B 374 SSBOND 1 CYS A 171 CYS A 371 1555 1555 2.08 SSBOND 2 CYS A 230 CYS A 395 1555 1555 2.09 SSBOND 3 CYS A 282 CYS A 331 1555 1555 2.08 SSBOND 4 CYS B 171 CYS B 371 1555 1555 2.05 SSBOND 5 CYS B 230 CYS B 395 1555 1555 2.04 SSBOND 6 CYS B 282 CYS B 331 1555 1555 2.05 CISPEP 1 THR A 38 PRO A 39 0 -0.60 CISPEP 2 LYS A 144 PRO A 145 0 6.13 CISPEP 3 GLY A 384 PRO A 385 0 2.13 CISPEP 4 THR B 38 PRO B 39 0 -4.46 CISPEP 5 LYS B 144 PRO B 145 0 11.00 CISPEP 6 GLY B 384 PRO B 385 0 4.51 SITE 1 AC1 14 LEU A 46 ASP A 48 PHE A 124 ILE A 134 SITE 2 AC1 14 TYR A 211 GLY A 243 ARG A 248 ALA A 342 SITE 3 AC1 14 HOH A2021 HOH A2023 HOH A2073 HOH A2093 SITE 4 AC1 14 HOH A2156 HOH A2157 CRYST1 46.887 88.466 98.572 90.00 96.58 90.00 P 1 21 1 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 0.021328 0.000000 0.002460 0.00000 SCALE2 0.000000 0.011304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010212 0.00000