HEADER HYDROLASE 02-OCT-09 3K3E TITLE CRYSTAL STRUCTURE OF THE PDE9A CATALYTIC DOMAIN IN COMPLEX WITH (R)- TITLE 2 BAY73-6691 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE COMPND 3 9A; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: CATALYTIC DOMAIN: UNP RESIDUES 241-566; COMPND 6 EC: 3.1.4.35; COMPND 7 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: PDE9A, PDE9A2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PDE9, CATALYTIC DOMAIN, CGMP, HYDROLASE, MANGANESE, METAL-BINDING, KEYWDS 2 PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,X.LUO,M.YE,J.HOU,H.ROBINSON,H.KE REVDAT 3 13-NOV-13 3K3E 1 HETATM HETNAM VERSN REVDAT 2 02-MAR-10 3K3E 1 JRNL REVDAT 1 16-FEB-10 3K3E 0 JRNL AUTH H.WANG,X.LUO,M.YE,J.HOU,H.ROBINSON,H.KE JRNL TITL INSIGHT INTO BINDING OF PHOSPHODIESTERASE-9A SELECTIVE JRNL TITL 2 INHIBITORS BY CRYSTAL STRUCTURES AND MUTAGENESIS JRNL REF J.MED.CHEM. V. 53 1726 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20121115 JRNL DOI 10.1021/JM901519F REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 39257 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3929 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5264 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055495. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41185 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.000 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 100.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SOAKING PDE9A2-IBMX CRYSTAL IN THE REMARK 280 BUFFER OF 0.1 M HEPES PH 7.5, 3.6 M SODIUM FORMATE, AND 2 MM REMARK 280 R6691 AT 25 DEG C FOR 3 DAYS. THE PDE9A2-IBMX CRYSTALS WERE GROWN REMARK 280 BY (1) MIXING 10-15 MG/ML PDE9A2 CATALYTIC DOMAIN (AMINO ACIDS REMARK 280 181-506) WITH 2 MM IBMX IN A BUFFER OF 50 MM NACL, 20 MM TRIS-HCL REMARK 280 PH 7.5, 1 MM BETA-MERCAPTOETHANOL, 1 MM EDTA, AND (2) THE VAPOR REMARK 280 DIFFUSION (HANGING DROP) AT 4 DEG C. THE PROTEIN DROPS CONTAINED REMARK 280 2 MICROLITERS PDE9A2-IBMX COMPLEX AND 2 MICROLITERS WELL SOLUTION REMARK 280 OF 0.1 M HEPES PH 7.5 AND 3.0 M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 135.42450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.71225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 203.13675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.71225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 203.13675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 135.42450 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL UNIT ASSEMBLY IS UNKNOWN. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 PRO A 181 REMARK 465 THR A 182 REMARK 465 TYR A 183 REMARK 465 PRO A 184 REMARK 465 LYS A 185 REMARK 465 TYR A 186 REMARK 465 PRO B 181 REMARK 465 THR B 182 REMARK 465 TYR B 183 REMARK 465 PRO B 184 REMARK 465 LYS B 185 REMARK 465 TYR B 186 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 LYS A 506 CA C O CB CG CD CE REMARK 470 LYS A 506 NZ REMARK 470 LYS B 506 CA C O CB CG CD CE REMARK 470 LYS B 506 NZ 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 251 -57.57 -120.85 REMARK 500 ASN A 300 -176.56 -66.18 REMARK 500 ASN A 316 49.32 37.89 REMARK 500 SER A 319 53.00 27.72 REMARK 500 ASN A 339 85.86 -65.07 REMARK 500 GLU A 380 -7.47 -51.96 REMARK 500 ASN A 381 75.03 173.61 REMARK 500 GLU A 434 -1.69 -145.55 REMARK 500 VAL A 460 -69.09 -142.63 REMARK 500 LYS A 505 74.83 -116.20 REMARK 500 LEU B 205 -71.53 -79.22 REMARK 500 TRP B 206 155.11 -46.61 REMARK 500 ARG B 226 -73.34 -50.76 REMARK 500 SER B 229 35.99 79.11 REMARK 500 PRO B 232 -18.38 -46.75 REMARK 500 PHE B 251 -62.11 -109.25 REMARK 500 HIS B 292 -29.66 -39.85 REMARK 500 SER B 319 54.15 31.21 REMARK 500 ASN B 339 74.46 -61.43 REMARK 500 ILE B 340 7.92 -61.95 REMARK 500 ASN B 343 35.53 -91.46 REMARK 500 ASN B 381 61.08 -164.65 REMARK 500 PHE B 382 164.43 -49.01 REMARK 500 ASP B 383 89.76 -162.84 REMARK 500 TYR B 384 2.02 -53.27 REMARK 500 PHE B 441 2.97 -67.73 REMARK 500 LYS B 446 -42.27 -135.07 REMARK 500 ALA B 450 -70.56 -51.89 REMARK 500 LYS B 505 -62.85 -120.91 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 256 NE2 REMARK 620 2 HIS A 292 NE2 93.9 REMARK 620 3 ASP A 293 OD2 83.1 77.7 REMARK 620 4 ASP A 402 OD1 93.9 79.7 156.9 REMARK 620 5 HOH A 702 O 171.8 94.0 96.3 89.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD1 REMARK 620 2 HOH A 705 O 89.5 REMARK 620 3 HOH A 706 O 106.9 100.0 REMARK 620 4 HOH A 702 O 95.1 75.5 157.6 REMARK 620 5 HOH A 703 O 163.7 75.6 82.6 75.0 REMARK 620 6 HOH A 704 O 112.6 144.2 99.9 74.8 77.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 256 NE2 REMARK 620 2 HIS B 292 NE2 86.0 REMARK 620 3 ASP B 293 OD2 84.9 76.1 REMARK 620 4 ASP B 402 OD1 88.4 81.4 156.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 293 OD1 REMARK 620 2 HOH B 715 O 88.2 REMARK 620 3 HOH B 713 O 86.5 80.6 REMARK 620 4 HOH B 714 O 147.7 73.9 64.5 REMARK 620 5 HOH B 712 O 114.2 65.0 138.0 82.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDB A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDB B 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K3H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDE9A CATALYTIC DOMAIN IN COMPLEX REMARK 900 WITH (S)-BAY73-6691 DBREF 3K3E A 181 506 UNP O76083 PDE9A_HUMAN 241 566 DBREF 3K3E B 181 506 UNP O76083 PDE9A_HUMAN 241 566 SEQRES 1 A 326 PRO THR TYR PRO LYS TYR LEU LEU SER PRO GLU THR ILE SEQRES 2 A 326 GLU ALA LEU ARG LYS PRO THR PHE ASP VAL TRP LEU TRP SEQRES 3 A 326 GLU PRO ASN GLU MET LEU SER CYS LEU GLU HIS MET TYR SEQRES 4 A 326 HIS ASP LEU GLY LEU VAL ARG ASP PHE SER ILE ASN PRO SEQRES 5 A 326 VAL THR LEU ARG ARG TRP LEU PHE CYS VAL HIS ASP ASN SEQRES 6 A 326 TYR ARG ASN ASN PRO PHE HIS ASN PHE ARG HIS CYS PHE SEQRES 7 A 326 CYS VAL ALA GLN MET MET TYR SER MET VAL TRP LEU CYS SEQRES 8 A 326 SER LEU GLN GLU LYS PHE SER GLN THR ASP ILE LEU ILE SEQRES 9 A 326 LEU MET THR ALA ALA ILE CYS HIS ASP LEU ASP HIS PRO SEQRES 10 A 326 GLY TYR ASN ASN THR TYR GLN ILE ASN ALA ARG THR GLU SEQRES 11 A 326 LEU ALA VAL ARG TYR ASN ASP ILE SER PRO LEU GLU ASN SEQRES 12 A 326 HIS HIS CYS ALA VAL ALA PHE GLN ILE LEU ALA GLU PRO SEQRES 13 A 326 GLU CYS ASN ILE PHE SER ASN ILE PRO PRO ASP GLY PHE SEQRES 14 A 326 LYS GLN ILE ARG GLN GLY MET ILE THR LEU ILE LEU ALA SEQRES 15 A 326 THR ASP MET ALA ARG HIS ALA GLU ILE MET ASP SER PHE SEQRES 16 A 326 LYS GLU LYS MET GLU ASN PHE ASP TYR SER ASN GLU GLU SEQRES 17 A 326 HIS MET THR LEU LEU LYS MET ILE LEU ILE LYS CYS CYS SEQRES 18 A 326 ASP ILE SER ASN GLU VAL ARG PRO MET GLU VAL ALA GLU SEQRES 19 A 326 PRO TRP VAL ASP CYS LEU LEU GLU GLU TYR PHE MET GLN SEQRES 20 A 326 SER ASP ARG GLU LYS SER GLU GLY LEU PRO VAL ALA PRO SEQRES 21 A 326 PHE MET ASP ARG ASP LYS VAL THR LYS ALA THR ALA GLN SEQRES 22 A 326 ILE GLY PHE ILE LYS PHE VAL LEU ILE PRO MET PHE GLU SEQRES 23 A 326 THR VAL THR LYS LEU PHE PRO MET VAL GLU GLU ILE MET SEQRES 24 A 326 LEU GLN PRO LEU TRP GLU SER ARG ASP ARG TYR GLU GLU SEQRES 25 A 326 LEU LYS ARG ILE ASP ASP ALA MET LYS GLU LEU GLN LYS SEQRES 26 A 326 LYS SEQRES 1 B 326 PRO THR TYR PRO LYS TYR LEU LEU SER PRO GLU THR ILE SEQRES 2 B 326 GLU ALA LEU ARG LYS PRO THR PHE ASP VAL TRP LEU TRP SEQRES 3 B 326 GLU PRO ASN GLU MET LEU SER CYS LEU GLU HIS MET TYR SEQRES 4 B 326 HIS ASP LEU GLY LEU VAL ARG ASP PHE SER ILE ASN PRO SEQRES 5 B 326 VAL THR LEU ARG ARG TRP LEU PHE CYS VAL HIS ASP ASN SEQRES 6 B 326 TYR ARG ASN ASN PRO PHE HIS ASN PHE ARG HIS CYS PHE SEQRES 7 B 326 CYS VAL ALA GLN MET MET TYR SER MET VAL TRP LEU CYS SEQRES 8 B 326 SER LEU GLN GLU LYS PHE SER GLN THR ASP ILE LEU ILE SEQRES 9 B 326 LEU MET THR ALA ALA ILE CYS HIS ASP LEU ASP HIS PRO SEQRES 10 B 326 GLY TYR ASN ASN THR TYR GLN ILE ASN ALA ARG THR GLU SEQRES 11 B 326 LEU ALA VAL ARG TYR ASN ASP ILE SER PRO LEU GLU ASN SEQRES 12 B 326 HIS HIS CYS ALA VAL ALA PHE GLN ILE LEU ALA GLU PRO SEQRES 13 B 326 GLU CYS ASN ILE PHE SER ASN ILE PRO PRO ASP GLY PHE SEQRES 14 B 326 LYS GLN ILE ARG GLN GLY MET ILE THR LEU ILE LEU ALA SEQRES 15 B 326 THR ASP MET ALA ARG HIS ALA GLU ILE MET ASP SER PHE SEQRES 16 B 326 LYS GLU LYS MET GLU ASN PHE ASP TYR SER ASN GLU GLU SEQRES 17 B 326 HIS MET THR LEU LEU LYS MET ILE LEU ILE LYS CYS CYS SEQRES 18 B 326 ASP ILE SER ASN GLU VAL ARG PRO MET GLU VAL ALA GLU SEQRES 19 B 326 PRO TRP VAL ASP CYS LEU LEU GLU GLU TYR PHE MET GLN SEQRES 20 B 326 SER ASP ARG GLU LYS SER GLU GLY LEU PRO VAL ALA PRO SEQRES 21 B 326 PHE MET ASP ARG ASP LYS VAL THR LYS ALA THR ALA GLN SEQRES 22 B 326 ILE GLY PHE ILE LYS PHE VAL LEU ILE PRO MET PHE GLU SEQRES 23 B 326 THR VAL THR LYS LEU PHE PRO MET VAL GLU GLU ILE MET SEQRES 24 B 326 LEU GLN PRO LEU TRP GLU SER ARG ASP ARG TYR GLU GLU SEQRES 25 B 326 LEU LYS ARG ILE ASP ASP ALA MET LYS GLU LEU GLN LYS SEQRES 26 B 326 LYS HET ZN A 601 1 HET MG A 602 1 HET PDB A 600 24 HET ZN B 601 1 HET MG B 602 1 HET PDB B 600 24 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM PDB 1-(2-CHLOROPHENYL)-6-[(2R)-3,3,3-TRIFLUORO-2- HETNAM 2 PDB METHYLPROPYL]-1,7-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN- HETNAM 3 PDB 4-ONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 PDB 2(C15 H12 CL F3 N4 O) FORMUL 9 HOH *16(H2 O) HELIX 1 1 SER A 189 LEU A 196 1 8 HELIX 2 2 GLU A 207 LEU A 222 1 16 HELIX 3 3 GLY A 223 PHE A 228 1 6 HELIX 4 4 ASN A 231 ASN A 245 1 15 HELIX 5 5 ASN A 253 CYS A 271 1 19 HELIX 6 6 SER A 272 LYS A 276 5 5 HELIX 7 7 SER A 278 HIS A 292 1 15 HELIX 8 8 ASN A 300 ALA A 307 1 8 HELIX 9 9 THR A 309 TYR A 315 1 7 HELIX 10 10 SER A 319 LEU A 333 1 15 HELIX 11 11 PRO A 345 ALA A 362 1 18 HELIX 12 12 THR A 363 ALA A 366 5 4 HELIX 13 13 ARG A 367 GLU A 380 1 14 HELIX 14 14 ASN A 386 ILE A 403 1 18 HELIX 15 15 SER A 404 ARG A 408 5 5 HELIX 16 16 PRO A 409 SER A 433 1 25 HELIX 17 17 ALA A 439 ASP A 443 5 5 HELIX 18 18 THR A 448 VAL A 460 1 13 HELIX 19 19 VAL A 460 LYS A 470 1 11 HELIX 20 20 PRO A 473 MET A 479 1 7 HELIX 21 21 MET A 479 GLN A 504 1 26 HELIX 22 22 SER B 189 LEU B 196 1 8 HELIX 23 23 GLU B 207 LEU B 222 1 16 HELIX 24 24 GLY B 223 SER B 229 1 7 HELIX 25 25 VAL B 233 ASN B 245 1 13 HELIX 26 26 ASN B 253 CYS B 271 1 19 HELIX 27 27 SER B 272 LYS B 276 5 5 HELIX 28 28 SER B 278 HIS B 292 1 15 HELIX 29 29 ASN B 300 ARG B 308 1 9 HELIX 30 30 THR B 309 ASN B 316 1 8 HELIX 31 31 SER B 319 LEU B 333 1 15 HELIX 32 32 PRO B 345 ALA B 362 1 18 HELIX 33 33 THR B 363 ALA B 366 5 4 HELIX 34 34 ARG B 367 MET B 379 1 13 HELIX 35 35 GLU B 380 PHE B 382 5 3 HELIX 36 36 ASN B 386 ILE B 403 1 18 HELIX 37 37 SER B 404 ARG B 408 5 5 HELIX 38 38 PRO B 409 GLY B 435 1 27 HELIX 39 39 ALA B 439 ASP B 443 5 5 HELIX 40 40 THR B 448 VAL B 460 1 13 HELIX 41 41 VAL B 460 PHE B 472 1 13 HELIX 42 42 MET B 474 MET B 479 1 6 HELIX 43 43 MET B 479 LEU B 503 1 25 SSBOND 1 CYS B 241 CYS B 338 1555 1555 2.05 LINK NE2 HIS A 256 ZN ZN A 601 1555 1555 2.09 LINK NE2 HIS A 292 ZN ZN A 601 1555 1555 2.10 LINK OD1 ASP A 293 MG MG A 602 1555 1555 2.10 LINK OD2 ASP A 293 ZN ZN A 601 1555 1555 2.05 LINK OD1 ASP A 402 ZN ZN A 601 1555 1555 2.06 LINK NE2 HIS B 256 ZN ZN B 601 1555 1555 2.10 LINK NE2 HIS B 292 ZN ZN B 601 1555 1555 2.11 LINK OD1 ASP B 293 MG MG B 602 1555 1555 2.13 LINK OD2 ASP B 293 ZN ZN B 601 1555 1555 2.05 LINK OD1 ASP B 402 ZN ZN B 601 1555 1555 2.06 LINK MG MG A 602 O HOH A 705 1555 1555 2.48 LINK MG MG A 602 O HOH A 706 1555 1555 2.32 LINK MG MG A 602 O HOH A 702 1555 1555 2.40 LINK MG MG B 602 O HOH B 715 1555 1555 2.43 LINK ZN ZN A 601 O HOH A 702 1555 1555 2.44 LINK MG MG A 602 O HOH A 703 1555 1555 2.53 LINK MG MG B 602 O HOH B 713 1555 1555 2.57 LINK MG MG A 602 O HOH A 704 1555 1555 2.64 LINK MG MG B 602 O HOH B 714 1555 1555 2.67 LINK MG MG B 602 O HOH B 712 1555 1555 2.78 SITE 1 AC1 6 HIS A 256 HIS A 292 ASP A 293 ASP A 402 SITE 2 AC1 6 HOH A 701 HOH A 702 SITE 1 AC2 6 ASP A 293 HOH A 702 HOH A 703 HOH A 704 SITE 2 AC2 6 HOH A 705 HOH A 706 SITE 1 AC3 9 HIS A 252 VAL A 417 LEU A 420 LEU A 421 SITE 2 AC3 9 TYR A 424 ALA A 452 GLN A 453 PHE A 456 SITE 3 AC3 9 HOH A 709 SITE 1 AC4 6 HIS B 256 HIS B 292 ASP B 293 ASP B 402 SITE 2 AC4 6 MG B 602 HOH B 711 SITE 1 AC5 6 ASP B 293 ZN B 601 HOH B 712 HOH B 713 SITE 2 AC5 6 HOH B 714 HOH B 715 SITE 1 AC6 7 HIS B 252 LEU B 420 LEU B 421 TYR B 424 SITE 2 AC6 7 ALA B 452 GLN B 453 PHE B 456 CRYST1 103.190 103.190 270.849 90.00 90.00 90.00 P 41 21 2 16 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 0.009691 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003692 0.00000