10 20 30 40 50 60 70 80 1XOZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 07-OCT-04 1XOZ
TITLE CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEX TITLE 2 WITH 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 COMPND 6 PHOSPHODIESTERASE, 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, AUTHOR 3 M.V.MILBURN,S.-H.KIM,J.SCHLESSINGER,K.Y.J.ZHANG
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, JRNL AUTH 2 B.LEE,C.LUU,M.TABRIZIZAD,S.GILLETTE,P.N.IBRAHIM, JRNL AUTH 3 D.R.ARTIS,G.BOLLAG,M.V.MILBURN,S.-H.KIM, JRNL AUTH 4 J.SCHLESSINGER,K.Y.J.ZHANG JRNL TITL STRUCTURAL BASIS FOR THE ACTIVITY OF DRUGS THAT JRNL TITL 2 INHIBIT 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 1
REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.25 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1095 ; 4.331 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1050 ; 6.453 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 1XOZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-04. REMARK 100 THE RCSB ID CODE IS RCSB030597.
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. = 7.6 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1327 DISTANCE = 5.54 ANGSTROMS
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 764 OD1 86.1 89.5 REMARK 620 4 HOH A1006 O 84.5 175.7 86.2 REMARK 620 5 ASP A 654 OD2 86.5 86.3 171.1 98.0 REMARK 620 6 HOH A1001 O 167.2 97.7 94.5 82.8 93.9 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 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 SEQADV 1XOZ SER A 661 UNP O76074 ASN 661 ENGINEERED SEQADV 1XOZ GLN A 663 UNP O76074 SER 663 ENGINEERED SEQADV 1XOZ LEU A 647 UNP O76074 ILE 664 ENGINEERED SEQADV 1XOZ ILE A 648 UNP O76074 GLN 665 ENGINEERED SEQADV 1XOZ ASN A 667 UNP O76074 ARG 667 ENGINEERED SEQADV 1XOZ THR A 668 UNP O76074 SER 668 ENGINEERED SEQADV 1XOZ ASN A 669 UNP O76074 GLU 669 ENGINEERED SEQADV 1XOZ SER A 670 UNP O76074 HIS 670 ENGINEERED SEQADV 1XOZ GLU A 671 UNP O76074 PRO 671 ENGINEERED SEQADV 1XOZ LEU A 674 UNP O76074 GLN 674 ENGINEERED SEQADV 1XOZ MET A 675 UNP O76074 LEU 675 ENGINEERED SEQADV 1XOZ ASN A 676A UNP O76074 CYS 677 ENGINEERED SEQADV 1XOZ ASP A 677 UNP O76074 ENGINEERED SEQADV 1XOZ GLU A 678 UNP O76074 HIS 678 ENGINEERED SEQADV 1XOZ VAL A 680 UNP O76074 ILE 680 ENGINEERED SEQADV 1XOZ LEU A 681 UNP O76074 MET 681 ENGINEERED
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 OD1 ASP A 764 1555 1555 2.08 LINK ZN ZN A 1 O HOH A1006 1555 1555 2.11 LINK ZN ZN A 1 OD2 ASP A 654 1555 1555 2.06 LINK ZN ZN A 1 O HOH A1001 1555 1555 2.04 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