PDB Short entry for 1XOZ HEADER HYDROLASE 07-OCT-04 1XOZ TITLE CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEX WITH TITLE 2 TADALAFIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A; COMPND 5 SYNONYM: CGB-PDE, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, COMPND 6 PDE5A; COMPND 7 EC: 3.1.4.17; COMPND 8 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: PDE5A, PDE5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON PLUS(RIL); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PHOSPHODIESTERASE, PDE, PDE5A, TADALAFIL, CIALIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.L.CARD,B.P.ENGLAND,Y.SUZUKI,D.FONG,B.POWELL,B.LEE,C.LUU, AUTHOR 2 M.TABRIZIZAD,S.GILLETTE,P.N.IBRAHIM,D.R.ARTIS,G.BOLLAG,M.V.MILBURN, AUTHOR 3 S.-H.KIM,J.SCHLESSINGER,K.Y.J.ZHANG REVDAT 4 20-OCT-21 1XOZ 1 REMARK SEQADV HETSYN LINK REVDAT 3 24-FEB-09 1XOZ 1 VERSN REVDAT 2 28-DEC-04 1XOZ 1 SEQADV REVDAT 1 14-DEC-04 1XOZ 0 JRNL AUTH G.L.CARD,B.P.ENGLAND,Y.SUZUKI,D.FONG,B.POWELL,B.LEE,C.LUU, JRNL AUTH 2 M.TABRIZIZAD,S.GILLETTE,P.N.IBRAHIM,D.R.ARTIS,G.BOLLAG, JRNL AUTH 3 M.V.MILBURN,S.-H.KIM,J.SCHLESSINGER,K.Y.J.ZHANG JRNL TITL STRUCTURAL BASIS FOR THE ACTIVITY OF DRUGS THAT INHIBIT JRNL TITL 2 PHOSPHODIESTERASES. JRNL REF STRUCTURE V. 12 2233 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15576036 JRNL DOI 10.1016/J.STR.2004.10.004 REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.25 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 64263 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3416 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4453 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2637 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.050 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2732 ; 0.024 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2466 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3681 ; 1.920 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5756 ; 1.114 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 4.517 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.199 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2981 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 529 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 673 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2863 ; 0.245 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1523 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 217 ; 0.193 ; 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): 30 ; 0.370 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 57 ; 0.302 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.342 ; 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): 1637 ; 1.807 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2631 ; 2.790 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1095 ; 4.331 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1050 ; 6.453 ; 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): 2732 ; 2.411 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 351 ; 6.552 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2669 ; 3.398 ; 2.000 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 : 1 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 534 A 858 REMARK 3 ORIGIN FOR THE GROUP (A): 37.0330 39.8790 20.5280 REMARK 3 T TENSOR REMARK 3 T11: 0.0375 T22: 0.0214 REMARK 3 T33: 0.0906 T12: -0.0047 REMARK 3 T13: 0.0375 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.1966 L22: 0.5414 REMARK 3 L33: 0.6899 L12: -0.1052 REMARK 3 L13: -0.1537 L23: 0.0851 REMARK 3 S TENSOR REMARK 3 S11: 0.0014 S12: -0.0359 S13: 0.0425 REMARK 3 S21: 0.0015 S22: 0.0042 S23: 0.0175 REMARK 3 S31: -0.0308 S32: -0.0447 S33: -0.0056 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 : 1.40 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 1XOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 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 : BLU-ICE REMARK 200 DATA SCALING SOFTWARE : ELVES REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 79.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.89400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: JEFFAMINE ED-2001, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.05100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.19850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.05100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.19850 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS ONE MONOMER. 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 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 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 MET A 513 REMARK 465 GLY A 514 REMARK 465 SER A 515 REMARK 465 SER A 516 REMARK 465 HIS A 517 REMARK 465 HIS A 518 REMARK 465 HIS A 519 REMARK 465 HIS A 520 REMARK 465 HIS A 521 REMARK 465 HIS A 522 REMARK 465 SER A 523 REMARK 465 SER A 524 REMARK 465 GLY A 525 REMARK 465 LEU A 526 REMARK 465 VAL A 527 REMARK 465 PRO A 528 REMARK 465 ARG A 529 REMARK 465 GLY A 530 REMARK 465 SER A 531 REMARK 465 HIS A 532 REMARK 465 MET A 533 REMARK 465 GLN A 859 REMARK 465 GLN A 860 REMARK 465 GLU A 861 REMARK 465 LYS A 862 REMARK 465 MET A 863 REMARK 465 LEU A 864 REMARK 465 ILE A 865 REMARK 465 ASN A 866 REMARK 465 GLY A 867 REMARK 465 GLU A 868 REMARK 465 SER A 869 REMARK 465 GLY A 870 REMARK 465 GLN A 871 REMARK 465 ALA A 872 REMARK 465 LYS A 873 REMARK 465 ARG A 874 REMARK 465 ASN A 875 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 A 1176 O HOH A 1348 1.74 REMARK 500 O HOH A 1051 O HOH A 1347 2.03 REMARK 500 O HOH A 1261 O HOH A 1331 2.03 REMARK 500 OD1 ASN A 609 O HOH A 1202 2.17 REMARK 500 CD LYS A 809 O HOH A 1060 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 663 O HOH A 1217 3545 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN A 635 CB GLN A 635 CG -0.227 REMARK 500 GLN A 635 CD GLN A 635 OE1 0.212 REMARK 500 GLN A 635 CD GLN A 635 NE2 0.196 REMARK 500 SER A 652 CB SER A 652 OG -0.095 REMARK 500 ARG A 794 NE ARG A 794 CZ -0.086 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 597 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 597 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 687 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 764 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 794 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 LEU A 826 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 ASP A 838 CB - CG - OD2 ANGL. DEV. = 5.7 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 LYS A 630 -79.05 -88.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 HOH 1001-1007 ARE ASSOCIATED WITH CHAIN A. 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 617 NE2 REMARK 620 2 HIS A 653 NE2 95.0 REMARK 620 3 ASP A 654 OD2 86.5 86.3 REMARK 620 4 ASP A 764 OD1 86.1 89.5 171.1 REMARK 620 5 HOH A1001 O 167.2 97.7 93.9 94.5 REMARK 620 6 HOH A1006 O 84.5 175.7 98.0 86.2 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 654 OD1 REMARK 620 2 HOH A1001 O 95.0 REMARK 620 3 HOH A1002 O 81.6 97.0 REMARK 620 4 HOH A1003 O 88.9 172.4 90.0 REMARK 620 5 HOH A1004 O 99.6 86.4 176.3 86.5 REMARK 620 6 HOH A1005 O 168.6 91.6 88.4 85.7 90.0 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIA A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XLX RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH CILOMILAST REMARK 900 RELATED ID: 1XLZ RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH FILAMINAST REMARK 900 RELATED ID: 1XM4 RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH PICLAMILAST REMARK 900 RELATED ID: 1XM6 RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH (R)-MESOPRAM REMARK 900 RELATED ID: 1XMU RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH ROFLUMILAST REMARK 900 RELATED ID: 1XMY RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH (R)-ROLIPRAM REMARK 900 RELATED ID: 1XN0 RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH (R,S)-ROLIPRAM REMARK 900 RELATED ID: 1XOM RELATED DB: PDB REMARK 900 PDE4D IN COMPLEX WITH CILOMILAST REMARK 900 RELATED ID: 1XON RELATED DB: PDB REMARK 900 PDE4D IN COMPLEX WITH PICLAMILAST REMARK 900 RELATED ID: 1XOQ RELATED DB: PDB REMARK 900 PDE4D IN COMPLEX WITH ROFLUMILAST REMARK 900 RELATED ID: 1XOR RELATED DB: PDB REMARK 900 PDE4D IN COMPLEX WITH ZARDAVERINE REMARK 900 RELATED ID: 1XOS RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH SILDENAFIL REMARK 900 RELATED ID: 1XOT RELATED DB: PDB REMARK 900 PDE4B IN COMPLEX WITH VARDENAFIL REMARK 900 RELATED ID: 1XP0 RELATED DB: PDB REMARK 900 PDE5A IN COMPLEX WITH VARDENAFIL DBREF 1XOZ A 534 875 UNP O76074 PDE5A_HUMAN 534 875 SEQADV 1XOZ MET A 513 UNP O76074 INITIATING METHIONINE SEQADV 1XOZ GLY A 514 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ SER A 515 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ SER A 516 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ HIS A 517 UNP O76074 EXPRESSION TAG SEQADV 1XOZ HIS A 518 UNP O76074 EXPRESSION TAG SEQADV 1XOZ HIS A 519 UNP O76074 EXPRESSION TAG SEQADV 1XOZ HIS A 520 UNP O76074 EXPRESSION TAG SEQADV 1XOZ HIS A 521 UNP O76074 EXPRESSION TAG SEQADV 1XOZ HIS A 522 UNP O76074 EXPRESSION TAG SEQADV 1XOZ SER A 523 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ SER A 524 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ GLY A 525 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ LEU A 526 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ VAL A 527 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ PRO A 528 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ ARG A 529 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ GLY A 530 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ SER A 531 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ HIS A 532 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ MET A 533 UNP O76074 CLONING ARTIFACT SEQADV 1XOZ PRO A 658 UNP O76074 ARG 658 ENGINEERED MUTATION SEQADV 1XOZ SER A 661 UNP O76074 ASN 661 ENGINEERED MUTATION SEQADV 1XOZ GLN A 663 UNP O76074 SER 663 ENGINEERED MUTATION SEQADV 1XOZ LEU A 647 UNP O76074 ILE 664 ENGINEERED MUTATION SEQADV 1XOZ ILE A 648 UNP O76074 GLN 665 ENGINEERED MUTATION SEQADV 1XOZ ASN A 667 UNP O76074 ARG 667 ENGINEERED MUTATION SEQADV 1XOZ THR A 668 UNP O76074 SER 668 ENGINEERED MUTATION SEQADV 1XOZ ASN A 669 UNP O76074 GLU 669 ENGINEERED MUTATION SEQADV 1XOZ SER A 670 UNP O76074 HIS 670 ENGINEERED MUTATION SEQADV 1XOZ GLU A 671 UNP O76074 PRO 671 ENGINEERED MUTATION SEQADV 1XOZ LEU A 674 UNP O76074 GLN 674 ENGINEERED MUTATION SEQADV 1XOZ MET A 675 UNP O76074 LEU 675 ENGINEERED MUTATION SEQADV 1XOZ ASN A 676A UNP O76074 CYS 677 ENGINEERED MUTATION SEQADV 1XOZ ASP A 677 UNP O76074 ENGINEERED MUTATION SEQADV 1XOZ GLU A 678 UNP O76074 HIS 678 ENGINEERED MUTATION SEQADV 1XOZ VAL A 680 UNP O76074 ILE 680 ENGINEERED MUTATION SEQADV 1XOZ LEU A 681 UNP O76074 MET 681 ENGINEERED MUTATION SEQRES 1 A 364 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 364 LEU VAL PRO ARG GLY SER HIS MET GLU GLU GLU THR ARG SEQRES 3 A 364 GLU LEU GLN SER LEU ALA ALA ALA VAL VAL PRO SER ALA SEQRES 4 A 364 GLN THR LEU LYS ILE THR ASP PHE SER PHE SER ASP PHE SEQRES 5 A 364 GLU LEU SER ASP LEU GLU THR ALA LEU CYS THR ILE ARG SEQRES 6 A 364 MET PHE THR ASP LEU ASN LEU VAL GLN ASN PHE GLN MET SEQRES 7 A 364 LYS HIS GLU VAL LEU CYS ARG TRP ILE LEU SER VAL LYS SEQRES 8 A 364 LYS ASN TYR ARG LYS ASN VAL ALA TYR HIS ASN TRP ARG SEQRES 9 A 364 HIS ALA PHE ASN THR ALA GLN CYS MET PHE ALA ALA LEU SEQRES 10 A 364 LYS ALA GLY LYS ILE GLN ASN LYS LEU THR ASP LEU GLU SEQRES 11 A 364 ILE LEU ALA LEU LEU ILE ALA ALA LEU SER HIS ASP LEU SEQRES 12 A 364 ASP HIS PRO GLY VAL SER ASN GLN PHE LEU ILE ASN THR SEQRES 13 A 364 ASN SER GLU LEU ALA LEU MET TYR ASN ASP GLU SER VAL SEQRES 14 A 364 LEU GLU HIS HIS HIS PHE ASP GLN CYS LEU MET ILE LEU SEQRES 15 A 364 ASN SER PRO GLY ASN GLN ILE LEU SER GLY LEU SER ILE SEQRES 16 A 364 GLU GLU TYR LYS THR THR LEU LYS ILE ILE LYS GLN ALA SEQRES 17 A 364 ILE LEU ALA THR ASP LEU ALA LEU TYR ILE LYS ARG ARG SEQRES 18 A 364 GLY GLU PHE PHE GLU LEU ILE ARG LYS ASN GLN PHE ASN SEQRES 19 A 364 LEU GLU ASP PRO HIS GLN LYS GLU LEU PHE LEU ALA MET SEQRES 20 A 364 LEU MET THR ALA CYS ASP LEU SER ALA ILE THR LYS PRO SEQRES 21 A 364 TRP PRO ILE GLN GLN ARG ILE ALA GLU LEU VAL ALA THR SEQRES 22 A 364 GLU PHE PHE ASP GLN GLY ASP ARG GLU ARG LYS GLU LEU SEQRES 23 A 364 ASN ILE GLU PRO THR ASP LEU MET ASN ARG GLU LYS LYS SEQRES 24 A 364 ASN LYS ILE PRO SER MET GLN VAL GLY PHE ILE ASP ALA SEQRES 25 A 364 ILE CYS LEU GLN LEU TYR GLU ALA LEU THR HIS VAL SER SEQRES 26 A 364 GLU ASP CYS PHE PRO LEU LEU ASP GLY CYS ARG LYS ASN SEQRES 27 A 364 ARG GLN LYS TRP GLN ALA LEU ALA GLU GLN GLN GLU LYS SEQRES 28 A 364 MET LEU ILE ASN GLY GLU SER GLY GLN ALA LYS ARG ASN HET ZN A 1 1 HET MG A 2 1 HET CIA A 501 29 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM CIA 6-BENZO[1,3]DIOXOL-5-YL-2-METHYL-2,3,6,7,12,12A- HETNAM 2 CIA HEXAHYDRO-PYRAZINO[1',2':1,6]PYRIDO[3,4-B]INDOLE-1,4- HETNAM 3 CIA DIONE HETSYN CIA TADALAFIL; CIALIS FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 CIA C22 H19 N3 O4 FORMUL 5 HOH *352(H2 O) HELIX 1 1 GLU A 534 ALA A 546 1 13 HELIX 2 2 SER A 550 LYS A 555 1 6 HELIX 3 3 SER A 567 LEU A 582 1 16 HELIX 4 4 ASN A 583 PHE A 588 1 6 HELIX 5 5 LYS A 591 ASN A 605 1 15 HELIX 6 6 ASN A 614 ALA A 631 1 18 HELIX 7 7 ILE A 634 LEU A 638 5 5 HELIX 8 8 THR A 639 HIS A 653 1 15 HELIX 9 9 SER A 661 THR A 668 1 8 HELIX 10 10 SER A 670 TYR A 676 1 7 HELIX 11 11 SER A 679 ASN A 694 1 16 HELIX 12 12 SER A 705 THR A 723 1 19 HELIX 13 13 ASP A 724 LYS A 741 1 18 HELIX 14 14 ASP A 748 LEU A 765 1 18 HELIX 15 15 SER A 766 LYS A 770 5 5 HELIX 16 16 PRO A 771 ASN A 798 1 28 HELIX 17 17 THR A 802 ASN A 811 5 10 HELIX 18 18 LYS A 812 ILE A 824 1 13 HELIX 19 19 ILE A 824 SER A 836 1 13 HELIX 20 20 CYS A 839 GLU A 858 1 20 LINK ZN ZN A 1 NE2 HIS A 617 1555 1555 2.12 LINK ZN ZN A 1 NE2 HIS A 653 1555 1555 2.14 LINK ZN ZN A 1 OD2 ASP A 654 1555 1555 2.06 LINK ZN ZN A 1 OD1 ASP A 764 1555 1555 2.08 LINK ZN ZN A 1 O HOH A1001 1555 1555 2.04 LINK ZN ZN A 1 O HOH A1006 1555 1555 2.11 LINK MG MG A 2 OD1 ASP A 654 1555 1555 2.08 LINK MG MG A 2 O HOH A1001 1555 1555 2.10 LINK MG MG A 2 O HOH A1002 1555 1555 2.11 LINK MG MG A 2 O HOH A1003 1555 1555 2.15 LINK MG MG A 2 O HOH A1004 1555 1555 2.10 LINK MG MG A 2 O HOH A1005 1555 1555 2.10 SITE 1 AC1 7 MG A 2 HIS A 617 HIS A 653 ASP A 654 SITE 2 AC1 7 ASP A 764 HOH A1001 HOH A1006 SITE 1 AC2 7 ZN A 1 ASP A 654 HOH A1001 HOH A1002 SITE 2 AC2 7 HOH A1003 HOH A1004 HOH A1005 SITE 1 AC3 12 ILE A 768 GLN A 775 VAL A 782 ALA A 783 SITE 2 AC3 12 PHE A 786 LEU A 804 ILE A 813 MET A 816 SITE 3 AC3 12 GLN A 817 PHE A 820 HOH A1128 HOH A1148 CRYST1 56.102 76.397 80.699 90.00 103.18 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017825 0.000000 0.004175 0.00000 SCALE2 0.000000 0.013089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012727 0.00000