PDB Short entry for 3ZKS HEADER HYDROLASE/IMMUNE SYSTEM 24-JAN-13 3ZKS TITLE BACE2 XAPERONE COMPLEX WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 2; COMPND 3 CHAIN: A; 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 MOL_ID: 2; COMPND 13 MOLECULE: XA4813; COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: 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); SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 10 ORGANISM_COMMON: LLAMA; SOURCE 11 ORGANISM_TAXID: 9844; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PMESY4 KEYWDS HYDROLASE-IMMUNE SYSTEM COMPLEX, INHIBITOR, NANOBODY EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,A.KUGLSTATTER,J.BENZ,M.STIHLE,A.RUF REVDAT 3 20-DEC-23 3ZKS 1 REMARK REVDAT 2 05-JUN-13 3ZKS 1 JRNL REVDAT 1 29-MAY-13 3ZKS 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. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 25928 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1383 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) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1878 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3635 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.73000 REMARK 3 B22 (A**2) : -1.97000 REMARK 3 B33 (A**2) : 2.70000 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): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.224 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.700 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3796 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5166 ; 1.449 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 472 ; 6.889 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;37.185 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 589 ;16.538 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.320 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 567 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2898 ; 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 : 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.HYDROGENS WERE USED BUT NOT OUTPUT. U VALUES REFINED REMARK 3 INDIVIDUALLY. REMARK 4 REMARK 4 3ZKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1290055628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28977 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 44.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.260 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 3ZKQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG1500 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 32.05050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.36050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.38200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.36050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.05050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.38200 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: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.3 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 ASP A 25 REMARK 465 SER A 26 REMARK 465 GLY A 27 REMARK 465 ARG A 28 REMARK 465 ALA A 173 REMARK 465 GLY A 174 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 ASN A 183 REMARK 465 ASN A 285 REMARK 465 SER A 286 REMARK 465 GLU A 287 REMARK 465 THR A 288 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 ALA A 398 REMARK 465 HIS D 272 REMARK 465 HIS D 273 REMARK 465 HIS D 274 REMARK 465 HIS D 275 REMARK 465 HIS D 276 REMARK 465 HIS D 277 REMARK 465 GLU D 278 REMARK 465 PRO D 279 REMARK 465 GLU D 280 REMARK 465 ALA D 281 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 D 2002 O HOH D 2038 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 TYR A 87 -161.59 -108.33 REMARK 500 TRP A 210 -88.23 -140.79 REMARK 500 LYS A 218 139.43 -176.22 REMARK 500 ASN A 227 66.64 -100.49 REMARK 500 ASP A 236 -73.10 -70.27 REMARK 500 LYS A 237 144.56 177.95 REMARK 500 ALA D 251 167.04 178.18 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 WZV A 1398 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZKG RELATED DB: PDB REMARK 900 BACE2 MUTANT APO STRUCTURE 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 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. REMARK 999 ANTIBODY RAISED IN LLAMA AGAINST BACE2. V(HH) EXPRESSED IN REMARK 999 E. COLI. WITH 6HIS AND EPEA TAG. DBREF 3ZKS A 13 398 UNP Q9Y5Z0 BACE2_HUMAN 75 460 DBREF 3ZKS D 160 281 PDB 3ZKS 3ZKS 160 281 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 122 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 122 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 122 PHE THR PHE SER SER ALA ILE MET THR TRP VAL ARG GLN SEQRES 4 D 122 ALA PRO GLY LYS GLY ARG GLU TRP VAL SER THR ILE GLY SEQRES 5 D 122 SER ASP GLY SER ILE THR THR TYR ALA ASP SER VAL LYS SEQRES 6 D 122 GLY ARG PHE THR ILE SER ARG ASP ASN ALA ARG ASN THR SEQRES 7 D 122 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 122 ALA VAL TYR TYR CYS THR SER ALA GLY ARG ARG GLY PRO SEQRES 9 D 122 GLY THR GLN VAL THR VAL SER SER HIS HIS HIS HIS HIS SEQRES 10 D 122 HIS GLU PRO GLU ALA HET WZV A1398 31 HETNAM WZV 5-(2,2,2-TRIFLUORO-ETHOXY)-PYRIDINE-2-CARBOXYLIC ACID HETNAM 2 WZV [3-((S)-2-AMINO-1,4-DIMETHYL-6-OXO-1,4,5,6-TETRAHYDRO- HETNAM 3 WZV PYRIMIDIN-4-YL)-PHENYL]-AMIDE FORMUL 3 WZV C20 H20 F3 N5 O3 FORMUL 4 HOH *150(H2 O) HELIX 1 1 ASN A 14 VAL A 19 5 6 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 CYS A 230 ALA A 235 1 6 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 LEU A 314 TYR A 318 1 5 HELIX 10 10 GLY A 346 GLU A 351 1 6 HELIX 11 11 THR D 187 ALA D 191 5 5 HELIX 12 12 ASN D 233 ARG D 235 5 3 HELIX 13 13 LYS D 246 THR D 250 5 5 SHEET 1 AA 2 LEU A 22 GLN A 23 0 SHEET 2 AA 2 TYR A 31 ILE A 36 -1 O TYR A 31 N GLN A 23 SHEET 1 AB 2 ARG A 77 TYR A 87 0 SHEET 2 AB 2 GLY A 90 THR A 102 -1 O GLY A 90 N TYR A 87 SHEET 1 AC 5 GLY A 185 LEU A 189 0 SHEET 2 AC 5 VAL A 165 MET A 170 -1 O SER A 167 N VAL A 188 SHEET 3 AC 5 PHE A 353 ASP A 358 -1 O VAL A 355 N MET A 168 SHEET 4 AC 5 ARG A 363 ALA A 368 -1 O ARG A 363 N ASP A 358 SHEET 5 AC 5 TRP A 202 PRO A 205 -1 O TRP A 202 N PHE A 366 SHEET 1 AD 5 GLN A 224 SER A 225 0 SHEET 2 AD 5 ILE A 216 ILE A 221 -1 O ILE A 221 N GLN A 224 SHEET 3 AD 5 ILE A 296 ARG A 301 -1 O SER A 297 N GLU A 220 SHEET 4 AD 5 ARG A 307 ILE A 313 -1 O PHE A 309 N LEU A 300 SHEET 5 AD 5 SER A 380 SER A 387 -1 O GLU A 381 N THR A 312 SHEET 1 AE 4 ALA A 238 VAL A 240 0 SHEET 2 AE 4 LEU A 343 ILE A 345 1 O LEU A 343 N ILE A 239 SHEET 3 AE 4 LEU A 247 PRO A 250 -1 O ARG A 248 N VAL A 344 SHEET 4 AE 4 ILE A 336 SER A 339 1 O SER A 337 N LEU A 249 SHEET 1 AF 3 ALA A 281 TRP A 283 0 SHEET 2 AF 3 GLU A 330 PHE A 334 -1 O GLU A 330 N TRP A 283 SHEET 3 AF 3 ILE A 319 PRO A 321 -1 O GLN A 320 N ARG A 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 DA 4 GLN D 162 SER D 166 0 SHEET 2 DA 4 LEU D 177 SER D 184 -1 O SER D 180 N SER D 166 SHEET 3 DA 4 THR D 237 MET D 242 -1 O LEU D 238 N CYS D 181 SHEET 4 DA 4 PHE D 227 ASP D 232 -1 O THR D 228 N GLN D 241 SHEET 1 DB 4 GLY D 169 VAL D 171 0 SHEET 2 DB 4 THR D 265 VAL D 269 1 O GLN D 266 N GLY D 169 SHEET 3 DB 4 ALA D 251 SER D 257 -1 O ALA D 251 N VAL D 267 SHEET 4 DB 4 ARG D 260 ARG D 261 -1 O ARG D 260 N SER D 257 SHEET 1 DC 6 GLY D 169 VAL D 171 0 SHEET 2 DC 6 THR D 265 VAL D 269 1 O GLN D 266 N GLY D 169 SHEET 3 DC 6 ALA D 251 SER D 257 -1 O ALA D 251 N VAL D 267 SHEET 4 DC 6 MET D 193 GLN D 198 -1 O THR D 194 N THR D 256 SHEET 5 DC 6 GLU D 205 ILE D 210 -1 O GLU D 205 N ARG D 197 SHEET 6 DC 6 THR D 217 TYR D 219 -1 O THR D 218 N THR D 209 SHEET 1 DD 2 ARG D 260 ARG D 261 0 SHEET 2 DD 2 ALA D 251 SER D 257 -1 O SER D 257 N ARG D 260 SSBOND 1 CYS A 171 CYS A 371 1555 1555 2.09 SSBOND 2 CYS A 230 CYS A 395 1555 1555 2.07 SSBOND 3 CYS A 282 CYS A 331 1555 1555 2.07 SSBOND 4 CYS D 181 CYS D 255 1555 1555 2.07 CISPEP 1 THR A 38 PRO A 39 0 -9.56 CISPEP 2 LYS A 144 PRO A 145 0 1.96 CISPEP 3 GLY A 384 PRO A 385 0 3.72 CISPEP 4 GLN D 160 VAL D 161 0 2.99 SITE 1 AC1 11 GLY A 29 TYR A 30 ASP A 48 TRP A 131 SITE 2 AC1 11 ASP A 241 SER A 242 GLY A 243 THR A 244 SITE 3 AC1 11 THR A 245 ALA A 347 GLU A 351 CRYST1 64.101 74.764 108.721 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 0.015600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009198 0.00000