HEADER HYDROLASE 23-MAY-06 2H44
TITLE CRYSTAL STRUCTURE OF PDE5A1 IN COMPLEX WITH ICARISID II
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 535-860;
COMPND 5 SYNONYM: CGB-PDE, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE;
COMPND 6 EC: 3.1.4.35;
COMPND 7 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 ICARISID II, FLAVONOID, PDE5A INHIBITOR, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.WANG,H.KE
REVDAT 4 30-AUG-23 2H44 1 REMARK LINK
REVDAT 3 24-FEB-09 2H44 1 VERSN
REVDAT 2 08-AUG-06 2H44 1 JRNL
REVDAT 1 06-JUN-06 2H44 0
JRNL AUTH H.WANG,Y.LIU,Q.HUAI,J.CAI,R.ZORAGHI,S.H.FRANCIS,J.D.CORBIN,
JRNL AUTH 2 H.ROBINSON,Z.XIN,G.LIN,H.KE
JRNL TITL MULTIPLE CONFORMATIONS OF PHOSPHODIESTERASE-5: IMPLICATIONS
JRNL TITL 2 FOR ENZYME FUNCTION AND DRUG 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 2
REMARK 2 RESOLUTION. 1.80 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) : 1.80
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) (%) : 9.7
REMARK 3 NUMBER OF REFLECTIONS : 35094
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) : 0.206
REMARK 3 FREE R VALUE : 0.233
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 3415
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 : 2650
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 39
REMARK 3 SOLVENT ATOMS : 231
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00
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) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.310
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC
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 : ICARIIN.PARAM
REMARK 3 PARAMETER FILE 3 : ION.PARAM
REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.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 2H44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-06.
REMARK 100 THE DEPOSITION ID IS D_1000037905.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-SEP-04
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 : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36177
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
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 : 11.40
REMARK 200 R MERGE (I) : 0.06100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.45600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1RKP
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.52
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2 MM ICARISID II MIXED WITH 15 MG/ML
REMARK 280 PROTEIN OVERNIGHT, CRYSTALLIZED AGAINST A WELL BUFFER OF 0.1 M
REMARK 280 HEPES, 12% PEG3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
REMARK 290 7555 Y,X,-Z+1/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+2/3
REMARK 290 10555 -Y,-X,-Z+5/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+1/6
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 35.38633
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 70.77267
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 53.07950
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 88.46583
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 17.69317
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 35.38633
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 70.77267
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 88.46583
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 53.07950
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 17.69317
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 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 OE1 GLU A 796 OE1 GLU A 796 12555 1.89
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 ASP A 656 45.36 -94.84
REMARK 500 GLN A 859 99.70 67.38
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 TYR A 676 0.06 SIDE CHAIN
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 HOH A 1 O
REMARK 620 2 HOH A 2 O 77.1
REMARK 620 3 HIS A 617 NE2 167.6 90.9
REMARK 620 4 HIS A 653 NE2 93.5 170.6 98.5
REMARK 620 5 ASP A 654 OD2 91.3 92.3 92.2 87.8
REMARK 620 6 ASP A 764 OD1 92.5 89.4 84.3 91.0 176.0
REMARK 620 N 1 2 3 4 5
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 HOH A 1 O
REMARK 620 2 HOH A 2 O 59.1
REMARK 620 3 HOH A 3 O 55.9 90.3
REMARK 620 4 HOH A 4 O 157.6 125.1 101.8
REMARK 620 5 ASP A 654 OD1 69.9 100.6 107.4 125.0
REMARK 620 N 1 2 3 4
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
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7CA A 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2H40 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF UNLIGANDED PDE5
REMARK 900 RELATED ID: 2H42 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF PDE5 IN COMPLEX WITH SILDENAFIL
DBREF 2H44 A 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
HET ZN A 501 1
HET MG A 502 1
HET 7CA A 301 37
HETNAM ZN ZINC ION
HETNAM MG MAGNESIUM ION
HETNAM 7CA 5,7-DIHYDROXY-2-(4-METHOXYPHENYL)-8-(3-METHYLBUTYL)-4-
HETNAM 2 7CA OXO-4H-CHROMEN-3-YL 6-DEOXY-ALPHA-L-MANNOPYRANOSIDE
HETSYN 7CA ICARISID II
FORMUL 2 ZN ZN 2+
FORMUL 3 MG MG 2+
FORMUL 4 7CA C27 H32 O10
FORMUL 5 HOH *231(H2 O)
HELIX 1 1 THR A 537 ALA A 546 1 10
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 HIS A 684 ASN A 694 1 11
HELIX 10 10 SER A 705 THR A 723 1 19
HELIX 11 11 ASP A 724 LYS A 741 1 18
HELIX 12 12 ASP A 748 LEU A 765 1 18
HELIX 13 13 SER A 766 LYS A 770 5 5
HELIX 14 14 PRO A 771 ASN A 798 1 28
HELIX 15 15 THR A 802 ASN A 811 5 10
HELIX 16 16 LYS A 812 CYS A 825 1 14
HELIX 17 17 CYS A 825 SER A 836 1 12
HELIX 18 18 CYS A 839 GLU A 858 1 20
SHEET 1 A 2 SER A 663 GLN A 666 0
SHEET 2 A 2 LEU A 675 HIS A 678 -1 O CYS A 677 N TYR A 664
LINK O HOH A 1 ZN ZN A 501 1555 1555 2.28
LINK O HOH A 1 MG MG A 502 1555 1555 2.97
LINK O HOH A 2 ZN ZN A 501 1555 1555 2.23
LINK O HOH A 2 MG MG A 502 1555 1555 2.71
LINK O HOH A 3 MG MG A 502 1555 1555 2.78
LINK O HOH A 4 MG MG A 502 1555 1555 2.79
LINK ZN ZN A 501 NE2 HIS A 617 1555 1555 2.11
LINK ZN ZN A 501 NE2 HIS A 653 1555 1555 2.10
LINK ZN ZN A 501 OD2 ASP A 654 1555 1555 2.06
LINK ZN ZN A 501 OD1 ASP A 764 1555 1555 2.06
LINK MG MG A 502 OD1 ASP A 654 1555 1555 2.89
SITE 1 AC1 6 HOH A 1 HOH A 2 HIS A 617 HIS A 653
SITE 2 AC1 6 ASP A 654 ASP A 764
SITE 1 AC2 6 HOH A 1 HOH A 2 HOH A 3 HOH A 4
SITE 2 AC2 6 HIS A 613 ASP A 654
SITE 1 AC3 24 HOH A 2 HOH A 3 HOH A 5 HOH A 26
SITE 2 AC3 24 HOH A 127 TYR A 612 HIS A 613 ASN A 661
SITE 3 AC3 24 SER A 663 TYR A 664 ILE A 665 SER A 668
SITE 4 AC3 24 LEU A 725 ASP A 764 LEU A 765 ALA A 767
SITE 5 AC3 24 ILE A 768 GLN A 775 ALA A 779 VAL A 782
SITE 6 AC3 24 LEU A 804 MET A 816 GLN A 817 PHE A 820
CRYST1 110.746 110.746 106.159 90.00 90.00 120.00 P 61 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 0.009030 0.005213 0.000000 0.00000
SCALE2 0.000000 0.010427 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009420 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
