10 20 30 40 50 60 70 80 2H42 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 23-MAY-06 2H42
TITLE CRYSTAL STRUCTURE OF PDE5 IN COMPLEX WITH SILDENAFIL
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 535-860; COMPND 5 SYNONYM: CGB-PDE, CGMP-BINDING CGMP-SPECIFIC COMPND 6 PHOSPHODIESTERASE; COMPND 7 EC: 3.1.4.35; 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 BL21; 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 VIAGRA, PDE5, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.WANG,H.KE
REVDAT 3 24-FEB-09 2H42 1 VERSN REVDAT 2 08-AUG-06 2H42 1 JRNL REVDAT 1 06-JUN-06 2H42 0
JRNL AUTH H.WANG,Y.LIU,Q.HUAI,J.CAI,R.ZORAGHI,S.H.FRANCIS, JRNL AUTH 2 J.D.CORBIN,H.ROBINSON,Z.XIN,G.LIN,H.KE JRNL TITL MULTIPLE CONFORMATIONS OF PHOSPHODIESTERASE-5: JRNL TITL 2 IMPLICATIONS FOR ENZYME FUNCTION AND DRUG JRNL TITL 3 DEVELOPMENT JRNL REF J.BIOL.CHEM. V. 281 21469 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16735511 JRNL DOI 10.1074/JBC.M512527200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 66315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 6432 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 311 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.17 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : VIAA.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2H42 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-06. REMARK 100 THE RCSB ID CODE IS RCSB037903.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-03 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 : NSLS REMARK 200 BEAMLINE : X29A 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68786 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 16.000 REMARK 200 R MERGE (I) : 0.11700 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1RKP REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MM SILDENAFIL MIXED WITH 15 MG/ML REMARK 280 PDE5A1 OVERNIGHT, CRYSTALLIZED AGAINST A WELL BUFFER OF 1.0 M REMARK 280 SODIUM CITRATE, 2.5% ETHANOL, 0.1 M HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 128.75133 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 64.37567 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 0.00000 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 128.75133 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 64.37567 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 128.75133 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 64.37567 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 128.75133 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 0.00000 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 64.37567 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: BIOLOGICAL UNIT MAY BE A MONOMER. HOWEVER, THE REMARK 300 CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS 3 MOLECULES.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 285.05226 REMARK 350 BIOMT3 2 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 SER B 668 REMARK 465 GLU B 669 REMARK 465 HIS B 670 REMARK 465 PRO B 671 REMARK 465 LEU B 672 REMARK 465 ALA B 673 REMARK 465 GLN B 674 REMARK 465 LEU B 675 REMARK 465 TYR B 676 REMARK 465 SER C 668 REMARK 465 GLU C 669 REMARK 465 HIS C 670 REMARK 465 PRO C 671 REMARK 465 LEU C 672 REMARK 465 ALA C 673 REMARK 465 GLN C 674 REMARK 465 LEU C 675 REMARK 465 TYR C 676
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 GLN A 589 65.98 38.77 REMARK 500 LYS A 630 -76.92 -84.84 REMARK 500 CYS A 677 126.43 -27.86 REMARK 500 SER A 766 -8.75 -52.78 REMARK 500 GLN A 859 94.64 45.00 REMARK 500 TYR B 612 -53.25 -121.81 REMARK 500 LYS B 630 -81.44 -82.65 REMARK 500 HIS B 678 -78.66 -112.58 REMARK 500 GLN B 859 104.13 67.37 REMARK 500 LYS C 630 -79.85 -87.71 REMARK 500 ASN C 636 0.03 -66.79 REMARK 500 HIS C 678 33.44 -143.82 REMARK 500 SER C 766 -7.17 -54.58 REMARK 500 GLN C 859 76.80 66.05 REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 617 NE2 REMARK 620 2 ASP A 654 OD2 98.2 REMARK 620 3 HIS A 653 NE2 106.2 86.2 REMARK 620 4 ASP A 764 OD1 79.6 172.5 87.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 654 OD1 REMARK 620 2 HOH A 111 O 78.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 764 OD1 REMARK 620 2 HIS B 617 NE2 76.1 REMARK 620 3 ASP B 654 OD2 165.2 106.2 REMARK 620 4 HIS B 653 NE2 88.6 109.8 76.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 654 OD1 REMARK 620 2 HOH B 254 O 54.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 764 OD1 REMARK 620 2 ASP C 654 OD2 170.5 REMARK 620 3 HIS C 653 NE2 94.5 76.1 REMARK 620 4 HIS C 617 NE2 74.8 110.1 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 124 O REMARK 620 2 HOH C 255 O 134.0 REMARK 620 3 ASP C 654 OD1 99.1 83.9 REMARK 620 N 1 2
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 501 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 503 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 504 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 505 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 506 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIA A 901 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIA B 902 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIA C 903
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H40 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PDE5 IN COMPLEX WITH SILDENAFIL REMARK 900 RELATED ID: 2H44 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF UNLIGANDED PDE5
DBREF 2H42 A 535 860 UNP O76074 PDE5A_HUMAN 535 860 DBREF 2H42 B 535 860 UNP O76074 PDE5A_HUMAN 535 860 DBREF 2H42 C 535 860 UNP O76074 PDE5A_HUMAN 535 860
SEQRES 1 A 326 GLU GLU THR ARG GLU LEU GLN SER LEU ALA ALA ALA VAL SEQRES 2 A 326 VAL PRO SER ALA GLN THR LEU LYS ILE THR ASP PHE SER SEQRES 3 A 326 PHE SER ASP PHE GLU LEU SER ASP LEU GLU THR ALA LEU SEQRES 4 A 326 CYS THR ILE ARG MET PHE THR ASP LEU ASN LEU VAL GLN SEQRES 5 A 326 ASN PHE GLN MET LYS HIS GLU VAL LEU CYS ARG TRP ILE SEQRES 6 A 326 LEU SER VAL LYS LYS ASN TYR ARG LYS ASN VAL ALA TYR SEQRES 7 A 326 HIS ASN TRP ARG HIS ALA PHE ASN THR ALA GLN CYS MET SEQRES 8 A 326 PHE ALA ALA LEU LYS ALA GLY LYS ILE GLN ASN LYS LEU SEQRES 9 A 326 THR ASP LEU GLU ILE LEU ALA LEU LEU ILE ALA ALA LEU SEQRES 10 A 326 SER HIS ASP LEU ASP HIS ARG GLY VAL ASN ASN SER TYR SEQRES 11 A 326 ILE GLN ARG SER GLU HIS PRO LEU ALA GLN LEU TYR CYS SEQRES 12 A 326 HIS SER ILE MET GLU HIS HIS HIS PHE ASP GLN CYS LEU SEQRES 13 A 326 MET ILE LEU ASN SER PRO GLY ASN GLN ILE LEU SER GLY SEQRES 14 A 326 LEU SER ILE GLU GLU TYR LYS THR THR LEU LYS ILE ILE SEQRES 15 A 326 LYS GLN ALA ILE LEU ALA THR ASP LEU ALA LEU TYR ILE SEQRES 16 A 326 LYS ARG ARG GLY GLU PHE PHE GLU LEU ILE ARG LYS ASN SEQRES 17 A 326 GLN PHE ASN LEU GLU ASP PRO HIS GLN LYS GLU LEU PHE SEQRES 18 A 326 LEU ALA MET LEU MET THR ALA CYS ASP LEU SER ALA ILE SEQRES 19 A 326 THR LYS PRO TRP PRO ILE GLN GLN ARG ILE ALA GLU LEU SEQRES 20 A 326 VAL ALA THR GLU PHE PHE ASP GLN GLY ASP ARG GLU ARG SEQRES 21 A 326 LYS GLU LEU ASN ILE GLU PRO THR ASP LEU MET ASN ARG SEQRES 22 A 326 GLU LYS LYS ASN LYS ILE PRO SER MET GLN VAL GLY PHE SEQRES 23 A 326 ILE ASP ALA ILE CYS LEU GLN LEU TYR GLU ALA LEU THR SEQRES 24 A 326 HIS VAL SER GLU ASP CYS PHE PRO LEU LEU ASP GLY CYS SEQRES 25 A 326 ARG LYS ASN ARG GLN LYS TRP GLN ALA LEU ALA GLU GLN SEQRES 26 A 326 GLN SEQRES 1 B 326 GLU GLU THR ARG GLU LEU GLN SER LEU ALA ALA ALA VAL SEQRES 2 B 326 VAL PRO SER ALA GLN THR LEU LYS ILE THR ASP PHE SER SEQRES 3 B 326 PHE SER ASP PHE GLU LEU SER ASP LEU GLU THR ALA LEU SEQRES 4 B 326 CYS THR ILE ARG MET PHE THR ASP LEU ASN LEU VAL GLN SEQRES 5 B 326 ASN PHE GLN MET LYS HIS GLU VAL LEU CYS ARG TRP ILE SEQRES 6 B 326 LEU SER VAL LYS LYS ASN TYR ARG LYS ASN VAL ALA TYR SEQRES 7 B 326 HIS ASN TRP ARG HIS ALA PHE ASN THR ALA GLN CYS MET SEQRES 8 B 326 PHE ALA ALA LEU LYS ALA GLY LYS ILE GLN ASN LYS LEU SEQRES 9 B 326 THR ASP LEU GLU ILE LEU ALA LEU LEU ILE ALA ALA LEU SEQRES 10 B 326 SER HIS ASP LEU ASP HIS ARG GLY VAL ASN ASN SER TYR SEQRES 11 B 326 ILE GLN ARG SER GLU HIS PRO LEU ALA GLN LEU TYR CYS SEQRES 12 B 326 HIS SER ILE MET GLU HIS HIS HIS PHE ASP GLN CYS LEU SEQRES 13 B 326 MET ILE LEU ASN SER PRO GLY ASN GLN ILE LEU SER GLY SEQRES 14 B 326 LEU SER ILE GLU GLU TYR LYS THR THR LEU LYS ILE ILE SEQRES 15 B 326 LYS GLN ALA ILE LEU ALA THR ASP LEU ALA LEU TYR ILE SEQRES 16 B 326 LYS ARG ARG GLY GLU PHE PHE GLU LEU ILE ARG LYS ASN SEQRES 17 B 326 GLN PHE ASN LEU GLU ASP PRO HIS GLN LYS GLU LEU PHE SEQRES 18 B 326 LEU ALA MET LEU MET THR ALA CYS ASP LEU SER ALA ILE SEQRES 19 B 326 THR LYS PRO TRP PRO ILE GLN GLN ARG ILE ALA GLU LEU SEQRES 20 B 326 VAL ALA THR GLU PHE PHE ASP GLN GLY ASP ARG GLU ARG SEQRES 21 B 326 LYS GLU LEU ASN ILE GLU PRO THR ASP LEU MET ASN ARG SEQRES 22 B 326 GLU LYS LYS ASN LYS ILE PRO SER MET GLN VAL GLY PHE SEQRES 23 B 326 ILE ASP ALA ILE CYS LEU GLN LEU TYR GLU ALA LEU THR SEQRES 24 B 326 HIS VAL SER GLU ASP CYS PHE PRO LEU LEU ASP GLY CYS SEQRES 25 B 326 ARG LYS ASN ARG GLN LYS TRP GLN ALA LEU ALA GLU GLN SEQRES 26 B 326 GLN SEQRES 1 C 326 GLU GLU THR ARG GLU LEU GLN SER LEU ALA ALA ALA VAL SEQRES 2 C 326 VAL PRO SER ALA GLN THR LEU LYS ILE THR ASP PHE SER SEQRES 3 C 326 PHE SER ASP PHE GLU LEU SER ASP LEU GLU THR ALA LEU SEQRES 4 C 326 CYS THR ILE ARG MET PHE THR ASP LEU ASN LEU VAL GLN SEQRES 5 C 326 ASN PHE GLN MET LYS HIS GLU VAL LEU CYS ARG TRP ILE SEQRES 6 C 326 LEU SER VAL LYS LYS ASN TYR ARG LYS ASN VAL ALA TYR SEQRES 7 C 326 HIS ASN TRP ARG HIS ALA PHE ASN THR ALA GLN CYS MET SEQRES 8 C 326 PHE ALA ALA LEU LYS ALA GLY LYS ILE GLN ASN LYS LEU SEQRES 9 C 326 THR ASP LEU GLU ILE LEU ALA LEU LEU ILE ALA ALA LEU SEQRES 10 C 326 SER HIS ASP LEU ASP HIS ARG GLY VAL ASN ASN SER TYR SEQRES 11 C 326 ILE GLN ARG SER GLU HIS PRO LEU ALA GLN LEU TYR CYS SEQRES 12 C 326 HIS SER ILE MET GLU HIS HIS HIS PHE ASP GLN CYS LEU SEQRES 13 C 326 MET ILE LEU ASN SER PRO GLY ASN GLN ILE LEU SER GLY SEQRES 14 C 326 LEU SER ILE GLU GLU TYR LYS THR THR LEU LYS ILE ILE SEQRES 15 C 326 LYS GLN ALA ILE LEU ALA THR ASP LEU ALA LEU TYR ILE SEQRES 16 C 326 LYS ARG ARG GLY GLU PHE PHE GLU LEU ILE ARG LYS ASN SEQRES 17 C 326 GLN PHE ASN LEU GLU ASP PRO HIS GLN LYS GLU LEU PHE SEQRES 18 C 326 LEU ALA MET LEU MET THR ALA CYS ASP LEU SER ALA ILE SEQRES 19 C 326 THR LYS PRO TRP PRO ILE GLN GLN ARG ILE ALA GLU LEU SEQRES 20 C 326 VAL ALA THR GLU PHE PHE ASP GLN GLY ASP ARG GLU ARG SEQRES 21 C 326 LYS GLU LEU ASN ILE GLU PRO THR ASP LEU MET ASN ARG SEQRES 22 C 326 GLU LYS LYS ASN LYS ILE PRO SER MET GLN VAL GLY PHE SEQRES 23 C 326 ILE ASP ALA ILE CYS LEU GLN LEU TYR GLU ALA LEU THR SEQRES 24 C 326 HIS VAL SER GLU ASP CYS PHE PRO LEU LEU ASP GLY CYS SEQRES 25 C 326 ARG LYS ASN ARG GLN LYS TRP GLN ALA LEU ALA GLU GLN SEQRES 26 C 326 GLN
HET ZN A 501 1 HET MG A 502 1 HET ZN B 503 1 HET MG B 504 1 HET ZN C 505 1 HET MG C 506 1 HET VIA A 901 33 HET VIA B 902 33 HET VIA C 903 33
HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM VIA 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL) HETNAM 2 VIA SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H- HETNAM 3 VIA PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
HETSYN VIA SILDENAFIL, VIAGRA
FORMUL 4 ZN 3(ZN 2+) FORMUL 5 MG 3(MG 2+) FORMUL 10 VIA 3(C22 H30 N6 O4 S) FORMUL 13 HOH *311(H2 O)
HELIX 1 1 GLU A 535 ALA A 546 1 12 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 LEU A 672 TYR A 676 5 5 HELIX 10 10 SER A 679 ASN A 694 1 16 HELIX 11 11 SER A 705 THR A 723 1 19 HELIX 12 12 ASP A 724 LYS A 741 1 18 HELIX 13 13 ASP A 748 SER A 766 1 19 HELIX 14 14 ALA A 767 LYS A 770 5 4 HELIX 15 15 PRO A 771 ASN A 798 1 28 HELIX 16 16 THR A 802 ASN A 811 5 10 HELIX 17 17 LYS A 812 ILE A 824 1 13 HELIX 18 18 ILE A 824 SER A 836 1 13 HELIX 19 19 CYS A 839 GLU A 858 1 20 HELIX 20 20 GLU B 535 ALA B 546 1 12 HELIX 21 21 SER B 550 LYS B 555 1 6 HELIX 22 22 SER B 567 LEU B 582 1 16 HELIX 23 23 ASN B 583 PHE B 588 1 6 HELIX 24 24 LYS B 591 ASN B 605 1 15 HELIX 25 25 ASN B 614 LYS B 630 1 17 HELIX 26 26 LYS B 633 LEU B 638 5 6 HELIX 27 27 THR B 639 HIS B 653 1 15 HELIX 28 28 SER B 679 ASN B 694 1 16 HELIX 29 29 SER B 705 ALA B 722 1 18 HELIX 30 30 ASP B 724 LYS B 741 1 18 HELIX 31 31 ASP B 748 LEU B 765 1 18 HELIX 32 32 SER B 766 LYS B 770 5 5 HELIX 33 33 PRO B 771 LEU B 797 1 27 HELIX 34 34 THR B 802 ASN B 811 5 10 HELIX 35 35 LYS B 812 ILE B 824 1 13 HELIX 36 36 ILE B 824 SER B 836 1 13 HELIX 37 37 CYS B 839 GLU B 858 1 20 HELIX 38 38 GLU C 535 ALA C 546 1 12 HELIX 39 39 SER C 550 LYS C 555 1 6 HELIX 40 40 SER C 567 LEU C 582 1 16 HELIX 41 41 ASN C 583 PHE C 588 1 6 HELIX 42 42 LYS C 591 ASN C 605 1 15 HELIX 43 43 ASN C 614 LYS C 630 1 17 HELIX 44 44 ILE C 634 LEU C 638 5 5 HELIX 45 45 THR C 639 HIS C 653 1 15 HELIX 46 46 SER C 679 ASN C 694 1 16 HELIX 47 47 SER C 705 THR C 723 1 19 HELIX 48 48 ASP C 724 LYS C 741 1 18 HELIX 49 49 ASP C 748 SER C 766 1 19 HELIX 50 50 ALA C 767 LYS C 770 5 4 HELIX 51 51 PRO C 771 ASN C 798 1 28 HELIX 52 52 THR C 802 ASN C 811 5 10 HELIX 53 53 LYS C 812 ILE C 824 1 13 HELIX 54 54 CYS C 825 SER C 836 1 12 HELIX 55 55 CYS C 839 GLU C 858 1 20
LINK ZN ZN A 501 NE2 HIS A 617 1555 1555 2.12 LINK ZN ZN A 501 OD2 ASP A 654 1555 1555 2.06 LINK ZN ZN A 501 NE2 HIS A 653 1555 1555 2.11 LINK ZN ZN A 501 OD1 ASP A 764 1555 1555 2.07 LINK MG MG A 502 OD1 ASP A 654 1555 1555 2.12 LINK MG MG A 502 O HOH A 111 1555 1555 2.58 LINK ZN ZN B 503 OD1 ASP B 764 1555 1555 2.06 LINK ZN ZN B 503 NE2 HIS B 617 1555 1555 2.13 LINK ZN ZN B 503 OD2 ASP B 654 1555 1555 2.07 LINK ZN ZN B 503 NE2 HIS B 653 1555 1555 2.12 LINK MG MG B 504 OD1 ASP B 654 1555 1555 2.11 LINK MG MG B 504 O HOH B 254 1555 1555 2.94 LINK ZN ZN C 505 OD1 ASP C 764 1555 1555 2.07 LINK ZN ZN C 505 OD2 ASP C 654 1555 1555 2.07 LINK ZN ZN C 505 NE2 HIS C 653 1555 1555 2.11 LINK ZN ZN C 505 NE2 HIS C 617 1555 1555 2.13 LINK MG MG C 506 O HOH C 124 1555 1555 3.03 LINK MG MG C 506 O HOH C 255 1555 1555 2.70 LINK MG MG C 506 OD1 ASP C 654 1555 1555 2.11
SITE 1 AC1 4 HIS A 617 HIS A 653 ASP A 654 ASP A 764 SITE 1 AC2 5 HOH A 111 HIS A 653 ASP A 654 GLU A 682 SITE 2 AC2 5 THR A 723 SITE 1 AC3 4 HIS B 617 HIS B 653 ASP B 654 ASP B 764 SITE 1 AC4 2 HOH B 254 ASP B 654 SITE 1 AC5 5 HOH C 255 HIS C 617 HIS C 653 ASP C 654 SITE 2 AC5 5 ASP C 764 SITE 1 AC6 4 HOH C 124 HOH C 255 ASP C 654 HIS C 657 SITE 1 AC7 7 HOH A 86 ASN A 661 ALA A 767 PHE A 786 SITE 2 AC7 7 LEU A 804 GLN A 817 PHE A 820 SITE 1 AC8 17 HIS A 670 PRO A 671 LEU A 672 HOH B 32 SITE 2 AC8 17 HOH B 72 HOH B 246 ASN B 661 ASN B 662 SITE 3 AC8 17 TYR B 664 ILE B 768 ALA B 779 VAL B 782 SITE 4 AC8 17 PHE B 786 LEU B 804 MET B 816 GLN B 817 SITE 5 AC8 17 PHE B 820 SITE 1 AC9 11 HOH C 71 HOH C 306 TYR C 612 ASN C 661 SITE 2 AC9 11 TYR C 664 ILE C 665 LEU C 725 PHE C 786 SITE 3 AC9 11 LEU C 804 GLN C 817 PHE C 820
CRYST1 164.575 164.575 193.127 90.00 90.00 120.00 P 62 2 2 36
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 0.006076 0.003508 0.000000 0.00000
SCALE2 0.000000 0.007016 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005178 0.00000