HEADER HYDROLASE 07-OCT-04 1XP0
TITLE CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEX WITH
TITLE 2 VARDENAFIL
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, VARDENAFIL, LEVITRA, 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 6 14-FEB-24 1XP0 1 REMARK
REVDAT 5 20-OCT-21 1XP0 1 REMARK SEQADV LINK
REVDAT 4 13-JUL-11 1XP0 1 VERSN
REVDAT 3 24-FEB-09 1XP0 1 VERSN
REVDAT 2 28-DEC-04 1XP0 1 SEQADV
REVDAT 1 14-DEC-04 1XP0 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. 1.79 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) : 1.79
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.70
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 3 NUMBER OF REFLECTIONS : 46654
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) : 0.194
REMARK 3 R VALUE (WORKING SET) : 0.193
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2521
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) : 1.79
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3311
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3830
REMARK 3 BIN FREE R VALUE SET COUNT : 179
REMARK 3 BIN FREE R VALUE : 0.3780
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 : 36
REMARK 3 SOLVENT ATOMS : 156
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.47
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.27000
REMARK 3 B22 (A**2) : 0.27000
REMARK 3 B33 (A**2) : -0.41000
REMARK 3 B12 (A**2) : 0.14000
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): 0.101
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.921
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966
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): 2735 ; 0.010 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 2480 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3683 ; 1.369 ; 1.967
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5788 ; 0.856 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 2.987 ; 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 ; 0.105 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2970 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 525 ; 0.004 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 616 ; 0.211 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2740 ; 0.224 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 1487 ; 0.085 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 125 ; 0.164 ; 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): 5 ; 0.113 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.277 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.134 ; 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 ; 0.611 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2631 ; 1.161 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1098 ; 2.253 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1052 ; 3.397 ; 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 : 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): -24.3410 39.8550 70.6240
REMARK 3 T TENSOR
REMARK 3 T11: 0.1479 T22: 0.0977
REMARK 3 T33: 0.1511 T12: -0.0901
REMARK 3 T13: -0.1368 T23: 0.0878
REMARK 3 L TENSOR
REMARK 3 L11: 0.9713 L22: 1.5150
REMARK 3 L33: 1.9555 L12: 0.1007
REMARK 3 L13: 0.6266 L23: -0.1226
REMARK 3 S TENSOR
REMARK 3 S11: 0.0726 S12: 0.0373 S13: -0.0493
REMARK 3 S21: 0.1195 S22: -0.1309 S23: -0.1335
REMARK 3 S31: -0.0463 S32: 0.1755 S33: 0.0583
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 1XP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-04.
REMARK 100 THE DEPOSITION ID IS D_1000030598.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-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 : 46654
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790
REMARK 200 RESOLUTION RANGE LOW (A) : 76.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9
REMARK 200 DATA REDUNDANCY : 6.000
REMARK 200 R MERGE (I) : 0.05800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9
REMARK 200 DATA REDUNDANCY IN SHELL : 5.50
REMARK 200 R MERGE FOR SHELL (I) : 0.59900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300
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 (%): 60.05
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, PH 7.0, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 148.00133
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.00067
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 111.00100
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.00033
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 185.00167
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 148.00133
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 74.00067
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 37.00033
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 111.00100
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 185.00167
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 1056 O HOH A 1148 2.02
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 ASP A 656 CB - CG - OD2 ANGL. DEV. = 5.5 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 -72.77 -91.74
REMARK 500 SER A 679 60.16 28.79
REMARK 500 LYS A 809 33.30 -95.84
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 99.3
REMARK 620 3 ASP A 654 OD2 87.1 90.2
REMARK 620 4 ASP A 764 OD1 86.7 87.0 172.7
REMARK 620 5 HOH A1001 O 165.9 94.8 93.8 93.2
REMARK 620 6 HOH A1006 O 85.0 172.0 96.7 86.5 80.9
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 93.3
REMARK 620 3 HOH A1002 O 80.9 98.9
REMARK 620 4 HOH A1003 O 93.5 170.8 88.3
REMARK 620 5 HOH A1004 O 96.9 85.2 175.5 87.9
REMARK 620 6 HOH A1005 O 168.0 92.4 87.8 82.1 94.1
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 VDN A 201
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: 1XOZ RELATED DB: PDB
REMARK 900 PDE5A IN COMPLEX WITH TADALAFIL
DBREF 1XP0 A 534 875 UNP O76074 PDE5A_HUMAN 534 875
SEQADV 1XP0 MET A 513 UNP O76074 INITIATING METHIONINE
SEQADV 1XP0 GLY A 514 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 SER A 515 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 SER A 516 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 HIS A 517 UNP O76074 EXPRESSION TAG
SEQADV 1XP0 HIS A 518 UNP O76074 EXPRESSION TAG
SEQADV 1XP0 HIS A 519 UNP O76074 EXPRESSION TAG
SEQADV 1XP0 HIS A 520 UNP O76074 EXPRESSION TAG
SEQADV 1XP0 HIS A 521 UNP O76074 EXPRESSION TAG
SEQADV 1XP0 HIS A 522 UNP O76074 EXPRESSION TAG
SEQADV 1XP0 SER A 523 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 SER A 524 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 GLY A 525 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 LEU A 526 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 VAL A 527 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 PRO A 528 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 ARG A 529 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 GLY A 530 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 SER A 531 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 HIS A 532 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 MET A 533 UNP O76074 CLONING ARTIFACT
SEQADV 1XP0 PRO A 658 UNP O76074 ARG 658 ENGINEERED MUTATION
SEQADV 1XP0 SER A 661 UNP O76074 ASN 661 ENGINEERED MUTATION
SEQADV 1XP0 GLN A 663 UNP O76074 ASN 663 ENGINEERED MUTATION
SEQADV 1XP0 LEU A 647 UNP O76074 SER 664 ENGINEERED MUTATION
SEQADV 1XP0 ILE A 648 UNP O76074 TYR 665 ENGINEERED MUTATION
SEQADV 1XP0 ASN A 667 UNP O76074 ARG 667 ENGINEERED MUTATION
SEQADV 1XP0 THR A 668 UNP O76074 SER 668 ENGINEERED MUTATION
SEQADV 1XP0 ASN A 669 UNP O76074 GLU 669 ENGINEERED MUTATION
SEQADV 1XP0 SER A 670 UNP O76074 HIS 670 ENGINEERED MUTATION
SEQADV 1XP0 GLU A 671 UNP O76074 PRO 671 ENGINEERED MUTATION
SEQADV 1XP0 LEU A 674 UNP O76074 GLN 674 ENGINEERED MUTATION
SEQADV 1XP0 MET A 675 UNP O76074 LEU 675 ENGINEERED MUTATION
SEQADV 1XP0 ASN A 676A UNP O76074 CYS 677 ENGINEERED MUTATION
SEQADV 1XP0 ASP A 677 UNP O76074 ENGINEERED MUTATION
SEQADV 1XP0 GLU A 678 UNP O76074 HIS 678 ENGINEERED MUTATION
SEQADV 1XP0 VAL A 680 UNP O76074 ILE 680 ENGINEERED MUTATION
SEQADV 1XP0 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 VDN A 201 34
HETNAM ZN ZINC ION
HETNAM MG MAGNESIUM ION
HETNAM VDN 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-
HETNAM 2 VDN 5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-
HETNAM 3 VDN ONE
HETSYN VDN VARDENAFIL, LEVITRA
FORMUL 2 ZN ZN 2+
FORMUL 3 MG MG 2+
FORMUL 4 VDN C23 H32 N6 O4 S
FORMUL 5 HOH *156(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 LEU A 797 1 27
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 CYS A 825 SER A 836 1 12
HELIX 20 20 CYS A 839 ALA A 857 1 19
LINK ZN ZN A 1 NE2 HIS A 617 1555 1555 2.10
LINK ZN ZN A 1 NE2 HIS A 653 1555 1555 2.04
LINK ZN ZN A 1 OD2 ASP A 654 1555 1555 2.10
LINK ZN ZN A 1 OD1 ASP A 764 1555 1555 2.09
LINK ZN ZN A 1 O HOH A1001 1555 1555 2.02
LINK ZN ZN A 1 O HOH A1006 1555 1555 1.97
LINK MG MG A 2 OD1 ASP A 654 1555 1555 2.16
LINK MG MG A 2 O HOH A1001 1555 1555 2.18
LINK MG MG A 2 O HOH A1002 1555 1555 2.09
LINK MG MG A 2 O HOH A1003 1555 1555 2.18
LINK MG MG A 2 O HOH A1004 1555 1555 2.13
LINK MG MG A 2 O HOH A1005 1555 1555 2.17
SITE 1 AC1 6 HIS A 617 HIS A 653 ASP A 654 ASP A 764
SITE 2 AC1 6 HOH A1001 HOH A1006
SITE 1 AC2 6 ASP A 654 HOH A1001 HOH A1002 HOH A1003
SITE 2 AC2 6 HOH A1004 HOH A1005
SITE 1 AC3 3 GLN A 817 PHE A 820 HOH A1007
CRYST1 89.662 89.662 222.002 90.00 90.00 120.00 P 65 2 2 12
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 0.011153 0.006439 0.000000 0.00000
SCALE2 0.000000 0.012878 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004504 0.00000