HEADER HYDROLASE/HYDROLASE INHIBITOR 21-MAY-10 3N3Z
TITLE CRYSTAL STRUCTURE OF PDE9A (E406A) MUTANT IN COMPLEX WITH IBMX
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 SYNONYM: PHOSPHODIESTERASE 9A;
COMPND 7 EC: 3.1.4.35;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PDE;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.HOU,H.-B.LUO,Y.CHEN,J.XU,R.ZHAO,L.ZOU
REVDAT 2 01-NOV-23 3N3Z 1 REMARK SEQADV LINK
REVDAT 1 13-APR-11 3N3Z 0
JRNL AUTH J.HOU,H.-B.LUO,Y.CHEN,J.XU,R.ZHAO,L.ZOU
JRNL TITL CRYSTAL STRUCTURE OF PDE9A (E406A) MUTATION IN COMPLEX WITH
JRNL TITL 2 IBMX
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0109
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) : 2.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.33
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3
REMARK 3 NUMBER OF REFLECTIONS : 34692
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) : 0.202
REMARK 3 R VALUE (WORKING SET) : 0.201
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1824
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) : 2.75
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2681
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43
REMARK 3 BIN R VALUE (WORKING SET) : 0.2730
REMARK 3 BIN FREE R VALUE SET COUNT : 138
REMARK 3 BIN FREE R VALUE : 0.3080
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5382
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 37
REMARK 3 SOLVENT ATOMS : 104
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.86
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.01000
REMARK 3 B22 (A**2) : 0.01000
REMARK 3 B33 (A**2) : -0.02000
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): 0.382
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.264
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.181
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.041
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5556 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7530 ; 1.140 ; 1.963
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 650 ; 4.846 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 274 ;35.151 ;24.307
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 994 ;16.882 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.531 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 812 ; 0.087 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4218 ; 0.005 ; 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): 3286 ; 0.529 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5360 ; 1.063 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2270 ; 1.465 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2170 ; 2.520 ; 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 : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 3N3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-10.
REMARK 100 THE DEPOSITION ID IS D_1000059350.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-APR-10
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 : SSRF
REMARK 200 BEAMLINE : BL17U
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36568
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750
REMARK 200 RESOLUTION RANGE LOW (A) : 38.330
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6
REMARK 200 DATA REDUNDANCY : 7.400
REMARK 200 R MERGE (I) : 0.11700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9
REMARK 200 DATA REDUNDANCY IN SHELL : 7.50
REMARK 200 R MERGE FOR SHELL (I) : 0.59000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2HD1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 74.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.75
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M NA FORMATE, 0.1M HEPES PH7.5, 5%
REMARK 280 XYLITOL, VAPOR DIFFUSION, 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 135.10500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.04500
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.04500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.55250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.04500
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.04500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 202.65750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.04500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.04500
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.55250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.04500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.04500
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 202.65750
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 135.10500
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: 2040 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 29730 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
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 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 95 O HOH B 100 2.10
REMARK 500 O HOH B 94 O HOH B 100 2.11
REMARK 500 O HOH A 91 O HOH A 92 2.12
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 SER A 319 52.04 31.92
REMARK 500 GLN A 504 -149.14 -93.79
REMARK 500 LYS A 505 -8.30 64.81
REMARK 500 ASP B 317 15.18 53.41
REMARK 500 SER B 319 57.10 31.80
REMARK 500 ILE B 340 -9.64 -58.64
REMARK 500 VAL B 460 -61.01 -99.65
REMARK 500 LYS B 505 -56.48 -120.18
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 MG A 508 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 89 O
REMARK 620 2 HOH A 90 O 98.3
REMARK 620 3 HOH A 91 O 77.2 112.7
REMARK 620 4 HOH A 92 O 124.4 72.2 59.2
REMARK 620 5 HOH A 93 O 86.8 170.0 59.8 97.8
REMARK 620 6 ASP A 293 OD1 93.8 112.1 135.0 141.2 75.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 507 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 292 NE2
REMARK 620 2 ASP A 293 OD2 78.2
REMARK 620 3 ASP A 402 OD1 69.4 146.5
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG B 1 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH B 94 O
REMARK 620 2 HOH B 95 O 82.5
REMARK 620 3 HOH B 96 O 159.9 78.2
REMARK 620 4 HOH B 97 O 83.7 71.4 84.7
REMARK 620 5 HOH B 100 O 58.2 57.8 114.3 118.0
REMARK 620 6 ASP B 293 OD1 107.5 145.3 85.6 76.7 155.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 2 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH B 94 O
REMARK 620 2 HIS B 292 NE2 104.8
REMARK 620 3 ASP B 293 OD2 107.9 76.8
REMARK 620 4 ASP B 402 OD1 72.5 73.5 149.1
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM B 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 508
DBREF 3N3Z A 181 506 UNP O76083 PDE9A_HUMAN 241 566
DBREF 3N3Z B 181 506 UNP O76083 PDE9A_HUMAN 241 566
SEQADV 3N3Z ALA A 406 UNP O76083 GLU 466 ENGINEERED MUTATION
SEQADV 3N3Z ALA B 406 UNP O76083 GLU 466 ENGINEERED MUTATION
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 ALA 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 ALA 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 IBM A 1 16
HET ZN A 507 1
HET MG A 508 1
HET ZN B 2 1
HET MG B 1 1
HET IBM B 507 16
HET CL B 508 1
HETNAM IBM 3-ISOBUTYL-1-METHYLXANTHINE
HETNAM ZN ZINC ION
HETNAM MG MAGNESIUM ION
HETNAM CL CHLORIDE ION
FORMUL 3 IBM 2(C10 H14 N4 O2)
FORMUL 4 ZN 2(ZN 2+)
FORMUL 5 MG 2(MG 2+)
FORMUL 9 CL CL 1-
FORMUL 10 HOH *104(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 ASN A 245 1 15
HELIX 6 6 ASN A 253 CYS A 271 1 19
HELIX 7 7 SER A 272 LYS A 276 5 5
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 TYR A 315 1 7
HELIX 11 11 SER A 319 ALA A 334 1 16
HELIX 12 12 PRO A 345 THR A 363 1 19
HELIX 13 13 ASP A 364 ALA A 366 5 3
HELIX 14 14 ARG A 367 GLU A 380 1 14
HELIX 15 15 ASN A 386 ILE A 403 1 18
HELIX 16 16 SER A 404 ARG A 408 5 5
HELIX 17 17 PRO A 409 GLU A 434 1 26
HELIX 18 18 ALA A 439 ASP A 443 5 5
HELIX 19 19 THR A 448 VAL A 460 1 13
HELIX 20 20 VAL A 460 LYS A 470 1 11
HELIX 21 21 MET A 474 MET A 479 1 6
HELIX 22 22 MET A 479 GLU A 502 1 24
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 ASN B 245 1 15
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 PRO B 473 MET B 479 1 7
HELIX 46 46 MET B 479 GLN B 504 1 26
LINK O HOH A 89 MG MG A 508 1555 1555 2.26
LINK O HOH A 90 MG MG A 508 1555 1555 2.12
LINK O HOH A 91 MG MG A 508 1555 1555 1.98
LINK O HOH A 92 MG MG A 508 1555 1555 2.28
LINK O HOH A 93 MG MG A 508 1555 1555 2.39
LINK NE2 HIS A 292 ZN ZN A 507 1555 1555 2.43
LINK OD2 ASP A 293 ZN ZN A 507 1555 1555 2.20
LINK OD1 ASP A 293 MG MG A 508 1555 1555 2.00
LINK OD1 ASP A 402 ZN ZN A 507 1555 1555 2.46
LINK MG MG B 1 O HOH B 94 1555 1555 2.26
LINK MG MG B 1 O HOH B 95 1555 1555 2.27
LINK MG MG B 1 O HOH B 96 1555 1555 2.04
LINK MG MG B 1 O HOH B 97 1555 1555 2.37
LINK MG MG B 1 O HOH B 100 1555 1555 2.05
LINK MG MG B 1 OD1 ASP B 293 1555 1555 2.20
LINK ZN ZN B 2 O HOH B 94 1555 1555 2.03
LINK ZN ZN B 2 NE2 HIS B 292 1555 1555 2.52
LINK ZN ZN B 2 OD2 ASP B 293 1555 1555 2.12
LINK ZN ZN B 2 OD1 ASP B 402 1555 1555 2.46
SITE 1 AC1 7 ILE A 403 ASN A 405 LEU A 420 TYR A 424
SITE 2 AC1 7 ALA A 452 GLN A 453 PHE A 456
SITE 1 AC2 5 HIS A 256 HIS A 292 ASP A 293 ASP A 402
SITE 2 AC2 5 MG A 508
SITE 1 AC3 7 HOH A 89 HOH A 90 HOH A 91 HOH A 92
SITE 2 AC3 7 HOH A 93 ASP A 293 ZN A 507
SITE 1 AC4 6 MG B 1 HOH B 94 HIS B 256 HIS B 292
SITE 2 AC4 6 ASP B 293 ASP B 402
SITE 1 AC5 7 ZN B 2 HOH B 94 HOH B 95 HOH B 96
SITE 2 AC5 7 HOH B 97 HOH B 100 ASP B 293
SITE 1 AC6 4 LEU B 420 TYR B 424 PHE B 441 PHE B 456
SITE 1 AC7 1 ARG B 487
CRYST1 104.090 104.090 270.210 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 0.009607 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009607 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003701 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
