HEADER HYDROLASE 06-OCT-04 1XOS
TITLE CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEX WITH
TITLE 2 SILDENAFIL
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B;
COMPND 5 SYNONYM: DPDE4, PDE32;
COMPND 6 EC: 3.1.4.17;
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: PDE4B;
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, PDE4B, SILDENAFIL, VIAGRA, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.L.CARD,B.P.ENGLAND,Y.SUZUKI,D.FONG,B.POWELL,B.LEE,C.LUU,
AUTHOR 2 M.TABRIZIZAD,S.GILLETTE,P.N.IBRAHIM,D.R.ARTIS,G.BOLLAG,M.V.MILBURN,
AUTHOR 3 S.-H.KIM,J.SCHLESSINGER,K.Y.J.ZHANG
REVDAT 4 20-NOV-24 1XOS 1 REMARK SEQADV HETSYN LINK
REVDAT 3 13-JUL-11 1XOS 1 VERSN
REVDAT 2 24-FEB-09 1XOS 1 VERSN
REVDAT 1 14-DEC-04 1XOS 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. 2.28 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) : 2.28
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.71
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 19916
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) : 0.212
REMARK 3 R VALUE (WORKING SET) : 0.210
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1080
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) : 2.28
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1413
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3750
REMARK 3 BIN FREE R VALUE SET COUNT : 78
REMARK 3 BIN FREE R VALUE : 0.4200
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2597
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 40
REMARK 3 SOLVENT ATOMS : 17
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) : 43.62
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.98000
REMARK 3 B22 (A**2) : 4.68000
REMARK 3 B33 (A**2) : -6.66000
REMARK 3 B12 (A**2) : 0.00000
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): 0.261
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.510
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2691 ; 0.016 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 2388 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3653 ; 1.538 ; 1.957
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5555 ; 1.099 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 6.138 ; 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): 411 ; 0.091 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2967 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 529 ; 0.005 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 629 ; 0.215 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2718 ; 0.223 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 1511 ; 0.112 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 50 ; 0.160 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.103 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 11 ; 0.253 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.343 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.096 ; 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): 1608 ; 0.711 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2601 ; 1.337 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1083 ; 1.996 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1052 ; 3.185 ; 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 : 5
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 162 A 193
REMARK 3 RESIDUE RANGE : A 195 A 319
REMARK 3 RESIDUE RANGE : A 321 A 367
REMARK 3 RESIDUE RANGE : A 370 A 431
REMARK 3 RESIDUE RANGE : A 433 A 485
REMARK 3 ORIGIN FOR THE GROUP (A): 2.5620 53.3550 42.5540
REMARK 3 T TENSOR
REMARK 3 T11: 0.0262 T22: 0.0263
REMARK 3 T33: 0.2870 T12: 0.0229
REMARK 3 T13: 0.0202 T23: 0.0353
REMARK 3 L TENSOR
REMARK 3 L11: 0.3490 L22: 1.9654
REMARK 3 L33: 4.5210 L12: -0.2702
REMARK 3 L13: -0.4179 L23: -0.9173
REMARK 3 S TENSOR
REMARK 3 S11: -0.0585 S12: 0.0213 S13: -0.1180
REMARK 3 S21: 0.1356 S22: 0.1888 S23: 0.1053
REMARK 3 S31: -0.1477 S32: -0.3030 S33: -0.1302
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 1XOS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-04.
REMARK 100 THE DEPOSITION ID IS D_1000030590.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-MAY-03
REMARK 200 TEMPERATURE (KELVIN) : 93
REMARK 200 PH : 10.0
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 : 19916
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280
REMARK 200 RESOLUTION RANGE LOW (A) : 70.710
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.07100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 5.20
REMARK 200 R MERGE FOR SHELL (I) : 0.01084
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
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 (%): 50.19
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE AND LITHIUM SULFATE ,
REMARK 280 PH 10.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X,-Y+1/2,Z
REMARK 290 7555 -X+1/2,Y,-Z
REMARK 290 8555 X,-Y,-Z+1/2
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 47.28550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.74050
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.55850
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.74050
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.28550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.55850
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 47.28550
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.55850
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.74050
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.55850
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.28550
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
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 44.74050
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 131
REMARK 465 GLY A 132
REMARK 465 SER A 133
REMARK 465 SER A 134
REMARK 465 HIS A 135
REMARK 465 HIS A 136
REMARK 465 HIS A 137
REMARK 465 HIS A 138
REMARK 465 HIS A 139
REMARK 465 HIS A 140
REMARK 465 SER A 141
REMARK 465 SER A 142
REMARK 465 GLY A 143
REMARK 465 LEU A 144
REMARK 465 VAL A 145
REMARK 465 PRO A 146
REMARK 465 ARG A 147
REMARK 465 GLY A 148
REMARK 465 SER A 149
REMARK 465 HIS A 150
REMARK 465 MET A 151
REMARK 465 SER A 152
REMARK 465 ILE A 153
REMARK 465 SER A 154
REMARK 465 ARG A 155
REMARK 465 PHE A 156
REMARK 465 GLY A 157
REMARK 465 VAL A 158
REMARK 465 ASN A 159
REMARK 465 THR A 160
REMARK 465 GLU A 161
REMARK 465 SER A 368
REMARK 465 SER A 369
REMARK 465 GLN A 486
REMARK 465 SER A 487
REMARK 465 PRO A 488
REMARK 465 SER A 489
REMARK 465 PRO A 490
REMARK 465 PRO A 491
REMARK 465 LEU A 492
REMARK 465 ASP A 493
REMARK 465 GLU A 494
REMARK 465 GLN A 495
REMARK 465 ASN A 496
REMARK 465 ARG A 497
REMARK 465 ASP A 498
REMARK 465 CYS A 499
REMARK 465 GLN A 500
REMARK 465 GLY A 501
REMARK 465 LEU A 502
REMARK 465 MET A 503
REMARK 465 GLU A 504
REMARK 465 LYS A 505
REMARK 465 PHE A 506
REMARK 465 GLN A 507
REMARK 465 PHE A 508
REMARK 465 GLU A 509
REMARK 465 LEU A 510
REMARK 465 THR A 511
REMARK 465 LEU A 512
REMARK 465 ASP A 513
REMARK 465 GLU A 514
REMARK 465 GLU A 515
REMARK 465 ASP A 516
REMARK 465 SER A 517
REMARK 465 GLU A 518
REMARK 465 GLY A 519
REMARK 465 PRO A 520
REMARK 465 GLU A 521
REMARK 465 LYS A 522
REMARK 465 GLU A 523
REMARK 465 GLY A 524
REMARK 465 GLU A 525
REMARK 465 GLY A 526
REMARK 465 HIS A 527
REMARK 465 SER A 528
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 210 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 318 CG CD OE1 OE2
REMARK 470 LEU A 373 CG CD1 CD2
REMARK 470 ASP A 375 CG OD1 OD2
REMARK 470 GLU A 427 CG CD OE1 OE2
REMARK 470 LYS A 441 CG CD CE NZ
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 164 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES
REMARK 500 ASP A 475 CB - CG - OD2 ANGL. DEV. = 7.6 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 GLU A 163 -36.52 -155.97
REMARK 500 ARG A 190 54.30 -116.51
REMARK 500 CME A 194 -75.14 -14.60
REMARK 500 HIS A 319 1.94 -61.41
REMARK 500 CME A 320 -6.99 -151.08
REMARK 500 THR A 327 153.33 -49.15
REMARK 500 VAL A 366 -157.95 -149.54
REMARK 500 LEU A 393 42.73 -101.14
REMARK 500 ILE A 450 -57.82 -130.77
REMARK 500 MET A 483 -5.91 -145.59
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 HOH 1003-1009 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 A1001 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 238 NE2
REMARK 620 2 HIS A 274 NE2 93.7
REMARK 620 3 ASP A 275 OD2 94.2 83.1
REMARK 620 4 ASP A 392 OD2 83.4 93.7 175.9
REMARK 620 5 HOH A1007 O 171.4 91.1 79.4 103.3
REMARK 620 6 HOH A1008 O 88.7 168.6 85.6 97.6 85.1
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A1002 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 275 OD1
REMARK 620 2 HOH A1003 O 76.9
REMARK 620 3 HOH A1004 O 78.1 83.8
REMARK 620 4 HOH A1005 O 161.8 87.7 90.8
REMARK 620 5 HOH A1006 O 83.9 87.1 161.2 105.3
REMARK 620 6 HOH A1007 O 84.7 160.5 98.7 111.5 84.7
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 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIA A 1
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 PDE4B IN COMPLEX WITH CILOMILAST
REMARK 900 RELATED ID: 1XON RELATED DB: PDB
REMARK 900 PDE4B IN COMPLEX WITH PICLAMILAST
REMARK 900 RELATED ID: 1XOQ RELATED DB: PDB
REMARK 900 PDE4B IN COMPLEX WITH ROFLUMILAST
REMARK 900 RELATED ID: 1XOR RELATED DB: PDB
REMARK 900 PDE4B IN COMPLEX WITH ZARDAVERINE
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
REMARK 900 RELATED ID: 1XP0 RELATED DB: PDB
REMARK 900 PDE5A IN COMPLEX WITH VARDENAFIL
DBREF 1XOS A 152 528 UNP Q07343 PDE4B_HUMAN 324 700
SEQADV 1XOS MET A 131 UNP Q07343 INITIATING METHIONINE
SEQADV 1XOS GLY A 132 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS SER A 133 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS SER A 134 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS HIS A 135 UNP Q07343 EXPRESSION TAG
SEQADV 1XOS HIS A 136 UNP Q07343 EXPRESSION TAG
SEQADV 1XOS HIS A 137 UNP Q07343 EXPRESSION TAG
SEQADV 1XOS HIS A 138 UNP Q07343 EXPRESSION TAG
SEQADV 1XOS HIS A 139 UNP Q07343 EXPRESSION TAG
SEQADV 1XOS HIS A 140 UNP Q07343 EXPRESSION TAG
SEQADV 1XOS SER A 141 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS SER A 142 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS GLY A 143 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS LEU A 144 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS VAL A 145 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS PRO A 146 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS ARG A 147 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS GLY A 148 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS SER A 149 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS HIS A 150 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS MET A 151 UNP Q07343 CLONING ARTIFACT
SEQADV 1XOS CME A 194 UNP Q07343 CYS 366 MODIFIED RESIDUE
SEQADV 1XOS CME A 320 UNP Q07343 CYS 492 MODIFIED RESIDUE
SEQADV 1XOS CME A 432 UNP Q07343 CYS 604 MODIFIED RESIDUE
SEQRES 1 A 398 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 398 LEU VAL PRO ARG GLY SER HIS MET SER ILE SER ARG PHE
SEQRES 3 A 398 GLY VAL ASN THR GLU ASN GLU ASP HIS LEU ALA LYS GLU
SEQRES 4 A 398 LEU GLU ASP LEU ASN LYS TRP GLY LEU ASN ILE PHE ASN
SEQRES 5 A 398 VAL ALA GLY TYR SER HIS ASN ARG PRO LEU THR CME ILE
SEQRES 6 A 398 MET TYR ALA ILE PHE GLN GLU ARG ASP LEU LEU LYS THR
SEQRES 7 A 398 PHE ARG ILE SER SER ASP THR PHE ILE THR TYR MET MET
SEQRES 8 A 398 THR LEU GLU ASP HIS TYR HIS SER ASP VAL ALA TYR HIS
SEQRES 9 A 398 ASN SER LEU HIS ALA ALA ASP VAL ALA GLN SER THR HIS
SEQRES 10 A 398 VAL LEU LEU SER THR PRO ALA LEU ASP ALA VAL PHE THR
SEQRES 11 A 398 ASP LEU GLU ILE LEU ALA ALA ILE PHE ALA ALA ALA ILE
SEQRES 12 A 398 HIS ASP VAL ASP HIS PRO GLY VAL SER ASN GLN PHE LEU
SEQRES 13 A 398 ILE ASN THR ASN SER GLU LEU ALA LEU MET TYR ASN ASP
SEQRES 14 A 398 GLU SER VAL LEU GLU ASN HIS HIS LEU ALA VAL GLY PHE
SEQRES 15 A 398 LYS LEU LEU GLN GLU GLU HIS CME ASP ILE PHE MET ASN
SEQRES 16 A 398 LEU THR LYS LYS GLN ARG GLN THR LEU ARG LYS MET VAL
SEQRES 17 A 398 ILE ASP MET VAL LEU ALA THR ASP MET SER LYS HIS MET
SEQRES 18 A 398 SER LEU LEU ALA ASP LEU LYS THR MET VAL GLU THR LYS
SEQRES 19 A 398 LYS VAL THR SER SER GLY VAL LEU LEU LEU ASP ASN TYR
SEQRES 20 A 398 THR ASP ARG ILE GLN VAL LEU ARG ASN MET VAL HIS CYS
SEQRES 21 A 398 ALA ASP LEU SER ASN PRO THR LYS SER LEU GLU LEU TYR
SEQRES 22 A 398 ARG GLN TRP THR ASP ARG ILE MET GLU GLU PHE PHE GLN
SEQRES 23 A 398 GLN GLY ASP LYS GLU ARG GLU ARG GLY MET GLU ILE SER
SEQRES 24 A 398 PRO MET CME ASP LYS HIS THR ALA SER VAL GLU LYS SER
SEQRES 25 A 398 GLN VAL GLY PHE ILE ASP TYR ILE VAL HIS PRO LEU TRP
SEQRES 26 A 398 GLU THR TRP ALA ASP LEU VAL GLN PRO ASP ALA GLN ASP
SEQRES 27 A 398 ILE LEU ASP THR LEU GLU ASP ASN ARG ASN TRP TYR GLN
SEQRES 28 A 398 SER MET ILE PRO GLN SER PRO SER PRO PRO LEU ASP GLU
SEQRES 29 A 398 GLN ASN ARG ASP CYS GLN GLY LEU MET GLU LYS PHE GLN
SEQRES 30 A 398 PHE GLU LEU THR LEU ASP GLU GLU ASP SER GLU GLY PRO
SEQRES 31 A 398 GLU LYS GLU GLY GLU GLY HIS SER
MODRES 1XOS CME A 194 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE
MODRES 1XOS CME A 320 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE
MODRES 1XOS CME A 432 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE
HET CME A 194 10
HET CME A 320 10
HET CME A 432 10
HET ZN A1001 1
HET MG A1002 1
HET SO4 A 2 5
HET VIA A 1 33
HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE
HETNAM ZN ZINC ION
HETNAM MG MAGNESIUM ION
HETNAM SO4 SULFATE 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 1 CME 3(C5 H11 N O3 S2)
FORMUL 2 ZN ZN 2+
FORMUL 3 MG MG 2+
FORMUL 4 SO4 O4 S 2-
FORMUL 5 VIA C22 H30 N6 O4 S
FORMUL 6 HOH *17(H2 O)
HELIX 1 1 GLU A 163 GLU A 171 1 9
HELIX 2 2 ASN A 179 TYR A 186 1 8
HELIX 3 3 ARG A 190 ARG A 203 1 14
HELIX 4 4 ASP A 204 PHE A 209 1 6
HELIX 5 5 SER A 212 HIS A 226 1 15
HELIX 6 6 ASN A 235 SER A 251 1 17
HELIX 7 7 THR A 252 ASP A 256 5 5
HELIX 8 8 THR A 260 HIS A 274 1 15
HELIX 9 9 SER A 282 THR A 289 1 8
HELIX 10 10 SER A 291 ASN A 298 1 8
HELIX 11 11 SER A 301 LEU A 314 1 14
HELIX 12 12 THR A 327 ALA A 344 1 18
HELIX 13 13 THR A 345 SER A 348 5 4
HELIX 14 14 LYS A 349 GLU A 362 1 14
HELIX 15 15 ASN A 376 LEU A 393 1 18
HELIX 16 16 SER A 394 LYS A 398 5 5
HELIX 17 17 SER A 399 GLU A 423 1 25
HELIX 18 18 SER A 429 ASP A 433 5 5
HELIX 19 19 SER A 438 ILE A 450 1 13
HELIX 20 20 ILE A 450 GLN A 463 1 14
HELIX 21 21 ALA A 466 SER A 482 1 17
LINK C THR A 193 N CME A 194 1555 1555 1.33
LINK C CME A 194 N ILE A 195 1555 1555 1.33
LINK C HIS A 319 N CME A 320 1555 1555 1.33
LINK C CME A 320 N ASP A 321 1555 1555 1.34
LINK C MET A 431 N CME A 432 1555 1555 1.33
LINK C CME A 432 N ASP A 433 1555 1555 1.34
LINK NE2 HIS A 238 ZN ZN A1001 1555 1555 2.17
LINK NE2 HIS A 274 ZN ZN A1001 1555 1555 2.22
LINK OD2 ASP A 275 ZN ZN A1001 1555 1555 2.16
LINK OD1 ASP A 275 MG MG A1002 1555 1555 2.16
LINK OD2 ASP A 392 ZN ZN A1001 1555 1555 2.20
LINK ZN ZN A1001 O HOH A1007 1555 1555 1.87
LINK ZN ZN A1001 O HOH A1008 1555 1555 2.34
LINK MG MG A1002 O HOH A1003 1555 1555 2.22
LINK MG MG A1002 O HOH A1004 1555 1555 2.21
LINK MG MG A1002 O HOH A1005 1555 1555 2.07
LINK MG MG A1002 O HOH A1006 1555 1555 2.02
LINK MG MG A1002 O HOH A1007 1555 1555 1.98
CISPEP 1 GLN A 463 PRO A 464 0 2.80
SITE 1 AC1 6 HIS A 238 HIS A 274 ASP A 275 ASP A 392
SITE 2 AC1 6 HOH A1007 HOH A1008
SITE 1 AC2 6 ASP A 275 HOH A1003 HOH A1004 HOH A1005
SITE 2 AC2 6 HOH A1006 HOH A1007
SITE 1 AC3 3 SER A 282 ASN A 283 GLN A 284
SITE 1 AC4 16 HOH A 10 TYR A 233 HIS A 234 MET A 347
SITE 2 AC4 16 ASP A 392 ASN A 395 ILE A 410 MET A 411
SITE 3 AC4 16 SER A 429 MET A 431 CME A 432 GLN A 443
SITE 4 AC4 16 PHE A 446 ILE A 450 HOH A1008 HOH A1009
CRYST1 94.571 107.117 89.481 90.00 90.00 90.00 I 21 21 21 8
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 0.010574 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009336 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011176 0.00000