PDB Short entry for 3DYN HEADER HYDROLASE 28-JUL-08 3DYN TITLE HUMAN PHOSPHODIESTRASE 9 IN COMPLEX WITH CGMP (ZN INHIBITED) 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 242-566; 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOPHODIESTRASE, ENZYME MECHANISM, CGMP, HYDROLASE, MANGANESE, METAL- KEYWDS 2 BINDING, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU,M.N.MANSOUR,K.DILLMAN,J.PEREZ,D.DANLEY,F.MENNITI REVDAT 5 30-AUG-23 3DYN 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3DYN 1 VERSN REVDAT 3 24-FEB-09 3DYN 1 VERSN REVDAT 2 23-SEP-08 3DYN 1 JRNL REVDAT 1 16-SEP-08 3DYN 0 JRNL AUTH S.LIU,M.N.MANSOUR,K.S.DILLMAN,J.R.PEREZ,D.E.DANLEY,P.A.AEED, JRNL AUTH 2 S.P.SIMONS,P.K.LEMOTTE,F.S.MENNITI JRNL TITL STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF HUMAN JRNL TITL 2 PHOSPHODIESTERASE 9. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 13309 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18757755 JRNL DOI 10.1073/PNAS.0708850105 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0008 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) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 77963 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 8759 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) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5595 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 632 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 450 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.49000 REMARK 3 B22 (A**2) : 1.49000 REMARK 3 B33 (A**2) : -2.97000 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.496 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5621 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3822 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7625 ; 1.120 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9316 ; 0.807 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 654 ; 6.147 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 278 ;34.403 ;24.317 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1000 ;16.630 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;20.959 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 821 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6145 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1127 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1369 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4007 ; 0.217 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2773 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2714 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 352 ; 0.205 ; 0.200 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): 6 ; 0.294 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 37 ; 0.240 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.202 ; 0.200 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): 4307 ; 2.171 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1288 ; 0.440 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5380 ; 2.362 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2710 ; 4.262 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2245 ; 6.133 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1479 ; 0.06 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 B (A): 2000 ; 0.10 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1479 ; 0.31 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 2000 ; 0.33 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 181 A 505 REMARK 3 ORIGIN FOR THE GROUP (A): 84.2591 45.6871 45.7531 REMARK 3 T TENSOR REMARK 3 T11: 0.0427 T22: -0.1211 REMARK 3 T33: -0.0131 T12: -0.0132 REMARK 3 T13: -0.0147 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.3748 L22: 0.4181 REMARK 3 L33: 0.5430 L12: -0.3538 REMARK 3 L13: -0.0500 L23: 0.0531 REMARK 3 S TENSOR REMARK 3 S11: 0.0746 S12: -0.0359 S13: -0.0322 REMARK 3 S21: -0.0264 S22: -0.0064 S23: 0.0513 REMARK 3 S31: -0.0589 S32: 0.0491 S33: -0.0682 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 181 B 505 REMARK 3 ORIGIN FOR THE GROUP (A): 92.8205 32.0538 6.9450 REMARK 3 T TENSOR REMARK 3 T11: -0.0066 T22: -0.0426 REMARK 3 T33: -0.0116 T12: 0.0413 REMARK 3 T13: 0.0020 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.1857 L22: 0.6893 REMARK 3 L33: 0.7949 L12: -0.1386 REMARK 3 L13: 0.0710 L23: -0.2808 REMARK 3 S TENSOR REMARK 3 S11: 0.0175 S12: 0.0919 S13: -0.0164 REMARK 3 S21: 0.0012 S22: -0.0267 S23: -0.0117 REMARK 3 S31: 0.0687 S32: 0.0279 S33: 0.0092 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 REMARK 4 REMARK 4 3DYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1TBM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 135.05900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.92850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.92850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.52950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.92850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.92850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 202.58850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.92850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.92850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.52950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.92850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.92850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 202.58850 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 135.05900 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 LYS A 506 REMARK 465 LYS B 506 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 CB CYS A 326 O HOH A 1231 1.74 REMARK 500 OE1 GLN B 481 O HOH B 988 1.86 REMARK 500 SG CYS A 326 O HOH A 1231 1.96 REMARK 500 OE2 GLU B 414 O HOH B 1109 2.02 REMARK 500 O HOH B 1015 O HOH B 1037 2.11 REMARK 500 NH1 ARG A 226 O HOH A 1125 2.15 REMARK 500 O HOH A 1204 O HOH A 1209 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 A 237 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 237 NE - CZ - NH2 ANGL. DEV. = -3.6 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 PRO A 184 150.92 -49.97 REMARK 500 ASP A 317 15.66 59.72 REMARK 500 SER A 319 58.36 28.81 REMARK 500 ASN A 381 75.27 -166.56 REMARK 500 ASP B 317 14.58 59.34 REMARK 500 SER B 319 59.08 34.42 REMARK 500 ASN B 381 71.96 -165.54 REMARK 500 GLN B 504 -86.59 -117.76 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 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 256 NE2 REMARK 620 2 HIS A 292 NE2 101.0 REMARK 620 3 ASP A 293 OD2 93.2 82.9 REMARK 620 4 ASP A 402 OD1 92.0 93.9 174.3 REMARK 620 5 HOH A1000 O 152.1 106.8 93.0 83.4 REMARK 620 6 HOH A1001 O 86.0 171.7 101.4 81.2 66.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD1 REMARK 620 2 HOH A1000 O 95.5 REMARK 620 3 HOH A1002 O 176.7 86.1 REMARK 620 4 HOH A1003 O 88.4 105.0 94.0 REMARK 620 5 HOH A1004 O 88.6 154.1 88.7 100.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 256 NE2 REMARK 620 2 HIS B 292 NE2 97.5 REMARK 620 3 ASP B 293 OD2 93.8 86.6 REMARK 620 4 ASP B 402 OD1 94.3 88.1 170.8 REMARK 620 5 HOH B 904 O 160.8 101.6 90.0 83.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 293 OD1 REMARK 620 2 PCG B 900 O2A 104.1 REMARK 620 3 HOH B 904 O 94.0 75.9 REMARK 620 4 HOH B 905 O 172.2 82.3 83.0 REMARK 620 5 HOH B 906 O 85.3 165.1 92.0 87.6 REMARK 620 6 HOH B 907 O 94.9 92.6 166.9 89.3 98.3 REMARK 620 N 1 2 3 4 5 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCG B 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DY8 RELATED DB: PDB REMARK 900 RELATED ID: 3DYL RELATED DB: PDB REMARK 900 RELATED ID: 3DYQ RELATED DB: PDB REMARK 900 RELATED ID: 3DYS RELATED DB: PDB DBREF 3DYN A 182 506 UNP O76083 PDE9A_HUMAN 242 566 DBREF 3DYN B 182 506 UNP O76083 PDE9A_HUMAN 242 566 SEQADV 3DYN GLY A 178 UNP O76083 EXPRESSION TAG SEQADV 3DYN SER A 179 UNP O76083 EXPRESSION TAG SEQADV 3DYN HIS A 180 UNP O76083 EXPRESSION TAG SEQADV 3DYN MET A 181 UNP O76083 EXPRESSION TAG SEQADV 3DYN GLY B 178 UNP O76083 EXPRESSION TAG SEQADV 3DYN SER B 179 UNP O76083 EXPRESSION TAG SEQADV 3DYN HIS B 180 UNP O76083 EXPRESSION TAG SEQADV 3DYN MET B 181 UNP O76083 EXPRESSION TAG SEQRES 1 A 329 GLY SER HIS MET THR TYR PRO LYS TYR LEU LEU SER PRO SEQRES 2 A 329 GLU THR ILE GLU ALA LEU ARG LYS PRO THR PHE ASP VAL SEQRES 3 A 329 TRP LEU TRP GLU PRO ASN GLU MET LEU SER CYS LEU GLU SEQRES 4 A 329 HIS MET TYR HIS ASP LEU GLY LEU VAL ARG ASP PHE SER SEQRES 5 A 329 ILE ASN PRO VAL THR LEU ARG ARG TRP LEU PHE CYS VAL SEQRES 6 A 329 HIS ASP ASN TYR ARG ASN ASN PRO PHE HIS ASN PHE ARG SEQRES 7 A 329 HIS CYS PHE CYS VAL ALA GLN MET MET TYR SER MET VAL SEQRES 8 A 329 TRP LEU CYS SER LEU GLN GLU LYS PHE SER GLN THR ASP SEQRES 9 A 329 ILE LEU ILE LEU MET THR ALA ALA ILE CYS HIS ASP LEU SEQRES 10 A 329 ASP HIS PRO GLY TYR ASN ASN THR TYR GLN ILE ASN ALA SEQRES 11 A 329 ARG THR GLU LEU ALA VAL ARG TYR ASN ASP ILE SER PRO SEQRES 12 A 329 LEU GLU ASN HIS HIS CYS ALA VAL ALA PHE GLN ILE LEU SEQRES 13 A 329 ALA GLU PRO GLU CYS ASN ILE PHE SER ASN ILE PRO PRO SEQRES 14 A 329 ASP GLY PHE LYS GLN ILE ARG GLN GLY MET ILE THR LEU SEQRES 15 A 329 ILE LEU ALA THR ASP MET ALA ARG HIS ALA GLU ILE MET SEQRES 16 A 329 ASP SER PHE LYS GLU LYS MET GLU ASN PHE ASP TYR SER SEQRES 17 A 329 ASN GLU GLU HIS MET THR LEU LEU LYS MET ILE LEU ILE SEQRES 18 A 329 LYS CYS CYS ASP ILE SER ASN GLU VAL ARG PRO MET GLU SEQRES 19 A 329 VAL ALA GLU PRO TRP VAL ASP CYS LEU LEU GLU GLU TYR SEQRES 20 A 329 PHE MET GLN SER ASP ARG GLU LYS SER GLU GLY LEU PRO SEQRES 21 A 329 VAL ALA PRO PHE MET ASP ARG ASP LYS VAL THR LYS ALA SEQRES 22 A 329 THR ALA GLN ILE GLY PHE ILE LYS PHE VAL LEU ILE PRO SEQRES 23 A 329 MET PHE GLU THR VAL THR LYS LEU PHE PRO MET VAL GLU SEQRES 24 A 329 GLU ILE MET LEU GLN PRO LEU TRP GLU SER ARG ASP ARG SEQRES 25 A 329 TYR GLU GLU LEU LYS ARG ILE ASP ASP ALA MET LYS GLU SEQRES 26 A 329 LEU GLN LYS LYS SEQRES 1 B 329 GLY SER HIS MET THR TYR PRO LYS TYR LEU LEU SER PRO SEQRES 2 B 329 GLU THR ILE GLU ALA LEU ARG LYS PRO THR PHE ASP VAL SEQRES 3 B 329 TRP LEU TRP GLU PRO ASN GLU MET LEU SER CYS LEU GLU SEQRES 4 B 329 HIS MET TYR HIS ASP LEU GLY LEU VAL ARG ASP PHE SER SEQRES 5 B 329 ILE ASN PRO VAL THR LEU ARG ARG TRP LEU PHE CYS VAL SEQRES 6 B 329 HIS ASP ASN TYR ARG ASN ASN PRO PHE HIS ASN PHE ARG SEQRES 7 B 329 HIS CYS PHE CYS VAL ALA GLN MET MET TYR SER MET VAL SEQRES 8 B 329 TRP LEU CYS SER LEU GLN GLU LYS PHE SER GLN THR ASP SEQRES 9 B 329 ILE LEU ILE LEU MET THR ALA ALA ILE CYS HIS ASP LEU SEQRES 10 B 329 ASP HIS PRO GLY TYR ASN ASN THR TYR GLN ILE ASN ALA SEQRES 11 B 329 ARG THR GLU LEU ALA VAL ARG TYR ASN ASP ILE SER PRO SEQRES 12 B 329 LEU GLU ASN HIS HIS CYS ALA VAL ALA PHE GLN ILE LEU SEQRES 13 B 329 ALA GLU PRO GLU CYS ASN ILE PHE SER ASN ILE PRO PRO SEQRES 14 B 329 ASP GLY PHE LYS GLN ILE ARG GLN GLY MET ILE THR LEU SEQRES 15 B 329 ILE LEU ALA THR ASP MET ALA ARG HIS ALA GLU ILE MET SEQRES 16 B 329 ASP SER PHE LYS GLU LYS MET GLU ASN PHE ASP TYR SER SEQRES 17 B 329 ASN GLU GLU HIS MET THR LEU LEU LYS MET ILE LEU ILE SEQRES 18 B 329 LYS CYS CYS ASP ILE SER ASN GLU VAL ARG PRO MET GLU SEQRES 19 B 329 VAL ALA GLU PRO TRP VAL ASP CYS LEU LEU GLU GLU TYR SEQRES 20 B 329 PHE MET GLN SER ASP ARG GLU LYS SER GLU GLY LEU PRO SEQRES 21 B 329 VAL ALA PRO PHE MET ASP ARG ASP LYS VAL THR LYS ALA SEQRES 22 B 329 THR ALA GLN ILE GLY PHE ILE LYS PHE VAL LEU ILE PRO SEQRES 23 B 329 MET PHE GLU THR VAL THR LYS LEU PHE PRO MET VAL GLU SEQRES 24 B 329 GLU ILE MET LEU GLN PRO LEU TRP GLU SER ARG ASP ARG SEQRES 25 B 329 TYR GLU GLU LEU LYS ARG ILE ASP ASP ALA MET LYS GLU SEQRES 26 B 329 LEU GLN LYS LYS HET ZN A 901 1 HET MG A 902 1 HET PCG A 903 23 HET ZN B 901 1 HET MG B 902 1 HET IBM B 903 16 HET PCG B 900 23 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM PCG CYCLIC GUANOSINE MONOPHOSPHATE HETNAM IBM 3-ISOBUTYL-1-METHYLXANTHINE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 PCG 2(C10 H12 N5 O7 P) FORMUL 8 IBM C10 H14 N4 O2 FORMUL 10 HOH *450(H2 O) HELIX 1 1 SER A 189 LEU A 196 1 8 HELIX 2 2 ASP A 202 TRP A 206 5 5 HELIX 3 3 GLU A 207 LEU A 222 1 16 HELIX 4 4 GLY A 223 SER A 229 1 7 HELIX 5 5 ASN A 231 TYR A 246 1 16 HELIX 6 6 ASN A 253 CYS A 271 1 19 HELIX 7 7 SER A 272 PHE A 277 1 6 HELIX 8 8 SER A 278 HIS A 292 1 15 HELIX 9 9 ASN A 300 ARG A 308 1 9 HELIX 10 10 THR A 309 ASN A 316 1 8 HELIX 11 11 SER A 319 ALA A 334 1 16 HELIX 12 12 GLU A 335 ASN A 339 5 5 HELIX 13 13 PRO A 345 THR A 363 1 19 HELIX 14 14 ASP A 364 ALA A 366 5 3 HELIX 15 15 ARG A 367 GLU A 380 1 14 HELIX 16 16 ASN A 386 ILE A 403 1 18 HELIX 17 17 SER A 404 ARG A 408 5 5 HELIX 18 18 PRO A 409 GLY A 435 1 27 HELIX 19 19 ALA A 439 ASP A 443 5 5 HELIX 20 20 THR A 448 VAL A 460 1 13 HELIX 21 21 VAL A 460 PHE A 472 1 13 HELIX 22 22 MET A 474 GLU A 502 1 29 HELIX 23 23 SER B 189 LEU B 196 1 8 HELIX 24 24 ASP B 202 TRP B 206 5 5 HELIX 25 25 GLU B 207 LEU B 222 1 16 HELIX 26 26 GLY B 223 SER B 229 1 7 HELIX 27 27 ASN B 231 TYR B 246 1 16 HELIX 28 28 ASN B 253 CYS B 271 1 19 HELIX 29 29 SER B 272 PHE B 277 1 6 HELIX 30 30 SER B 278 HIS B 292 1 15 HELIX 31 31 ASN B 300 ALA B 307 1 8 HELIX 32 32 THR B 309 ASN B 316 1 8 HELIX 33 33 SER B 319 GLU B 335 1 17 HELIX 34 34 PRO B 336 ASN B 339 5 4 HELIX 35 35 PRO B 345 ALA B 362 1 18 HELIX 36 36 THR B 363 ALA B 366 5 4 HELIX 37 37 ARG B 367 MET B 379 1 13 HELIX 38 38 GLU B 380 PHE B 382 5 3 HELIX 39 39 ASN B 386 ILE B 403 1 18 HELIX 40 40 SER B 404 ARG B 408 5 5 HELIX 41 41 PRO B 409 GLY B 435 1 27 HELIX 42 42 ALA B 439 ASP B 443 5 5 HELIX 43 43 THR B 448 VAL B 460 1 13 HELIX 44 44 VAL B 460 PHE B 472 1 13 HELIX 45 45 MET B 474 MET B 479 1 6 HELIX 46 46 MET B 479 LEU B 503 1 25 LINK NE2 HIS A 256 ZN ZN A 901 1555 1555 2.14 LINK NE2 HIS A 292 ZN ZN A 901 1555 1555 2.15 LINK OD2 ASP A 293 ZN ZN A 901 1555 1555 2.04 LINK OD1 ASP A 293 MG MG A 902 1555 1555 2.30 LINK OD1 ASP A 402 ZN ZN A 901 1555 1555 2.11 LINK ZN ZN A 901 O HOH A1000 1555 1555 2.26 LINK ZN ZN A 901 O HOH A1001 1555 1555 2.13 LINK MG MG A 902 O HOH A1000 1555 1555 2.34 LINK MG MG A 902 O HOH A1002 1555 1555 2.27 LINK MG MG A 902 O HOH A1003 1555 1555 2.17 LINK MG MG A 902 O HOH A1004 1555 1555 2.45 LINK NE2 HIS B 256 ZN ZN B 901 1555 1555 2.12 LINK NE2 HIS B 292 ZN ZN B 901 1555 1555 2.20 LINK OD2 ASP B 293 ZN ZN B 901 1555 1555 2.12 LINK OD1 ASP B 293 MG MG B 902 1555 1555 2.31 LINK OD1 ASP B 402 ZN ZN B 901 1555 1555 2.10 LINK O2A PCG B 900 MG MG B 902 1555 1555 2.37 LINK ZN ZN B 901 O HOH B 904 1555 1555 2.37 LINK MG MG B 902 O HOH B 904 1555 1555 2.37 LINK MG MG B 902 O HOH B 905 1555 1555 2.31 LINK MG MG B 902 O HOH B 906 1555 1555 2.37 LINK MG MG B 902 O HOH B 907 1555 1555 2.31 SITE 1 AC1 6 HIS A 256 HIS A 292 ASP A 293 ASP A 402 SITE 2 AC1 6 HOH A1000 HOH A1001 SITE 1 AC2 5 ASP A 293 HOH A1000 HOH A1002 HOH A1003 SITE 2 AC2 5 HOH A1004 SITE 1 AC3 5 HIS B 256 HIS B 292 ASP B 293 ASP B 402 SITE 2 AC3 5 HOH B 904 SITE 1 AC4 5 ASP B 293 HOH B 904 HOH B 905 HOH B 906 SITE 2 AC4 5 HOH B 907 SITE 1 AC5 17 HIS A 252 MET A 365 ILE A 403 LEU A 420 SITE 2 AC5 17 TYR A 424 ALA A 452 GLN A 453 PHE A 456 SITE 3 AC5 17 HOH A1000 HOH A1001 HOH A1017 HOH A1050 SITE 4 AC5 17 HOH A1064 HOH A1070 HOH A1112 HOH A1133 SITE 5 AC5 17 HOH A1196 SITE 1 AC6 7 ALA A 499 LEU A 503 LEU B 420 TYR B 424 SITE 2 AC6 7 ALA B 452 GLN B 453 PHE B 456 SITE 1 AC7 18 HIS B 252 HIS B 256 ASP B 293 MET B 365 SITE 2 AC7 18 ASP B 402 ILE B 403 LEU B 420 TYR B 424 SITE 3 AC7 18 ALA B 452 GLN B 453 PHE B 456 HOH B 904 SITE 4 AC7 18 HOH B 905 HOH B 913 HOH B 918 HOH B 933 SITE 5 AC7 18 HOH B 946 HOH B 994 CRYST1 103.857 103.857 270.118 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 0.009629 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003702 0.00000