HEADER HYDROLASE/INHIBITOR 24-NOV-16 5WQA TITLE CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN COMPLEXED WITH TITLE 2 SELAGINPULVILINS K COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 381-714; COMPND 5 SYNONYM: DPDE3,PDE43; COMPND 6 EC: 3.1.4.53; 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: PDE4D, DPDE3; 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 KEYWDS NATURAL PDE4 INHIBTOR, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.HUANG,T.ZHANG,X.ZHENG,S.YIN,H.B.LUO REVDAT 4 08-NOV-23 5WQA 1 LINK REVDAT 3 18-OCT-17 5WQA 1 REMARK REVDAT 2 05-APR-17 5WQA 1 JRNL REVDAT 1 22-FEB-17 5WQA 0 JRNL AUTH Y.HUANG,X.LIU,D.WU,G.TANG,Z.LAI,X.ZHENG,S.YIN,H.B.LUO JRNL TITL THE DISCOVERY, COMPLEX CRYSTAL STRUCTURE, AND RECOGNITION JRNL TITL 2 MECHANISM OF A NOVEL NATURAL PDE4 INHIBITOR FROM SELAGINELLA JRNL TITL 3 PULVINATA JRNL REF BIOCHEM. PHARMACOL. V. 130 51 2017 JRNL REFN ISSN 1873-2968 JRNL PMID 28159622 JRNL DOI 10.1016/J.BCP.2017.01.016 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32918 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2376 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 181 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.02000 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): 0.380 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.077 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5622 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5314 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7630 ; 1.097 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12200 ; 0.753 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 666 ; 4.867 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 278 ;35.475 ;25.036 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 984 ;14.042 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.130 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6298 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1302 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2670 ; 1.262 ; 2.866 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2669 ; 1.261 ; 2.866 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3334 ; 2.249 ; 4.286 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3335 ; 2.248 ; 4.287 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2952 ; 1.112 ; 2.927 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2953 ; 1.112 ; 2.927 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4297 ; 1.982 ; 4.347 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6840 ; 3.875 ;22.012 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6792 ; 3.840 ;22.051 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 5WQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 38.41 REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 38.41 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 81.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.10 REMARK 200 STARTING MODEL: 1XON REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH 7.4), 0.1M MGCL2, 15% REMARK 280 PEG3350, 10% ISOPROPANOL, 25% ETHYLENE GLYCOL, 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 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 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 28.99600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.78750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.39200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.78750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.99600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.39200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL 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 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL 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 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 SER A 294 18.15 -69.68 REMARK 500 SER A 295 22.66 -142.53 REMARK 500 LEU A 319 42.51 -101.71 REMARK 500 MET A 357 -4.49 73.59 REMARK 500 ASN A 362 70.21 -114.76 REMARK 500 SER A 364 70.26 -153.74 REMARK 500 ILE A 376 -67.76 -129.54 REMARK 500 THR B 86 -155.53 -82.39 REMARK 500 SER B 294 -1.15 82.31 REMARK 500 LEU B 319 42.28 -100.39 REMARK 500 MET B 357 -7.75 74.86 REMARK 500 SER B 364 70.84 -156.07 REMARK 500 ILE B 376 -59.95 -122.44 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 164 NE2 REMARK 620 2 HIS A 200 NE2 93.1 REMARK 620 3 ASP A 201 OD2 87.4 85.5 REMARK 620 4 ASP A 318 OD1 90.4 87.0 172.0 REMARK 620 5 HOH A 620 O 87.3 177.8 96.7 90.9 REMARK 620 6 HOH A 638 O 171.3 91.9 85.9 96.9 87.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 201 OD1 REMARK 620 2 HOH A 628 O 91.4 REMARK 620 3 HOH A 638 O 85.1 84.9 REMARK 620 4 HOH A 641 O 172.5 93.0 101.4 REMARK 620 5 HOH A 648 O 86.8 177.8 93.5 88.9 REMARK 620 6 HOH A 668 O 88.1 87.4 169.6 86.1 93.9 REMARK 620 N 1 2 3 4 5 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 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 97.8 REMARK 620 3 ASP B 201 OD2 90.2 84.4 REMARK 620 4 ASP B 318 OD1 90.1 84.8 169.2 REMARK 620 5 HOH B 610 O 88.0 170.7 103.0 87.8 REMARK 620 6 HOH B 634 O 170.5 90.0 85.1 96.1 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 609 O 78.8 REMARK 620 3 HOH B 614 O 85.2 86.1 REMARK 620 4 HOH B 628 O 94.7 86.3 172.2 REMARK 620 5 HOH B 634 O 93.0 171.5 95.6 92.2 REMARK 620 6 HOH B 647 O 171.1 93.9 89.4 89.7 94.5 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 J20 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue J20 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 503 DBREF 5WQA A 79 412 UNP Q08499 PDE4D_HUMAN 381 714 DBREF 5WQA B 79 412 UNP Q08499 PDE4D_HUMAN 381 714 SEQRES 1 A 334 ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP VAL SEQRES 2 A 334 LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY LEU SEQRES 3 A 334 HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG PRO SEQRES 4 A 334 LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG ASP SEQRES 5 A 334 LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU ILE SEQRES 6 A 334 THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA ASP SEQRES 7 A 334 VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL VAL SEQRES 8 A 334 GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU GLU SEQRES 9 A 334 ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE PHE SEQRES 10 A 334 ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SER SEQRES 11 A 334 ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA LEU SEQRES 12 A 334 MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS LEU SEQRES 13 A 334 ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS ASP SEQRES 14 A 334 ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER LEU SEQRES 15 A 334 ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP MET SEQRES 16 A 334 SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR MET SEQRES 17 A 334 VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU LEU SEQRES 18 A 334 LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN ASN SEQRES 19 A 334 MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS PRO SEQRES 20 A 334 LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET GLU SEQRES 21 A 334 GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG GLY SEQRES 22 A 334 MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SER SEQRES 23 A 334 VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE VAL SEQRES 24 A 334 HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS PRO SEQRES 25 A 334 ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN ARG SEQRES 26 A 334 GLU TRP TYR GLN SER THR ILE PRO GLN SEQRES 1 B 334 ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP VAL SEQRES 2 B 334 LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY LEU SEQRES 3 B 334 HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG PRO SEQRES 4 B 334 LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG ASP SEQRES 5 B 334 LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU ILE SEQRES 6 B 334 THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA ASP SEQRES 7 B 334 VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL VAL SEQRES 8 B 334 GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU GLU SEQRES 9 B 334 ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE PHE SEQRES 10 B 334 ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SER SEQRES 11 B 334 ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA LEU SEQRES 12 B 334 MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS LEU SEQRES 13 B 334 ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS ASP SEQRES 14 B 334 ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER LEU SEQRES 15 B 334 ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP MET SEQRES 16 B 334 SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR MET SEQRES 17 B 334 VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU LEU SEQRES 18 B 334 LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN ASN SEQRES 19 B 334 MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS PRO SEQRES 20 B 334 LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET GLU SEQRES 21 B 334 GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG GLY SEQRES 22 B 334 MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SER SEQRES 23 B 334 VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE VAL SEQRES 24 B 334 HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS PRO SEQRES 25 B 334 ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN ARG SEQRES 26 B 334 GLU TRP TYR GLN SER THR ILE PRO GLN HET J20 A 501 41 HET ZN A 502 1 HET MG A 503 1 HET J20 B 501 41 HET MG B 502 1 HET ZN B 503 1 HETNAM J20 1-[2-(4-HYDROXYPHENYL)ETHYNYL]-9,9-BIS(4- HETNAM 2 J20 METHOXYPHENYL)-7-OXIDANYL-FLUORENE-2-CARBALDEHYDE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 3 J20 2(C36 H26 O5) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *181(H2 O) HELIX 1 AA1 THR A 86 LEU A 96 1 11 HELIX 2 AA2 GLU A 97 VAL A 99 5 3 HELIX 3 AA3 HIS A 105 SER A 113 1 9 HELIX 4 AA4 ARG A 116 ARG A 129 1 14 HELIX 5 AA5 ASP A 130 PHE A 135 1 6 HELIX 6 AA6 PRO A 138 HIS A 152 1 15 HELIX 7 AA7 ASN A 161 SER A 177 1 17 HELIX 8 AA8 THR A 178 GLU A 182 5 5 HELIX 9 AA9 THR A 186 HIS A 200 1 15 HELIX 10 AB1 SER A 208 THR A 215 1 8 HELIX 11 AB2 SER A 217 ASN A 224 1 8 HELIX 12 AB3 SER A 227 LEU A 240 1 14 HELIX 13 AB4 LEU A 241 GLU A 243 5 3 HELIX 14 AB5 THR A 253 ALA A 270 1 18 HELIX 15 AB6 THR A 271 SER A 274 5 4 HELIX 16 AB7 LYS A 275 THR A 289 1 15 HELIX 17 AB8 ASN A 302 LEU A 319 1 18 HELIX 18 AB9 SER A 320 LYS A 324 5 5 HELIX 19 AC1 PRO A 325 ARG A 350 1 26 HELIX 20 AC2 SER A 364 ILE A 376 1 13 HELIX 21 AC3 ILE A 376 VAL A 388 1 13 HELIX 22 AC4 ALA A 392 ILE A 410 1 19 HELIX 23 AC5 GLU B 87 GLU B 97 1 11 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ASP B 130 1 15 HELIX 26 AC8 ASP B 130 PHE B 135 1 6 HELIX 27 AC9 PRO B 138 HIS B 152 1 15 HELIX 28 AD1 ASN B 161 SER B 177 1 17 HELIX 29 AD2 THR B 178 GLU B 182 5 5 HELIX 30 AD3 THR B 186 HIS B 200 1 15 HELIX 31 AD4 SER B 208 THR B 215 1 8 HELIX 32 AD5 SER B 217 ASN B 224 1 8 HELIX 33 AD6 SER B 227 LEU B 240 1 14 HELIX 34 AD7 LEU B 241 GLU B 243 5 3 HELIX 35 AD8 THR B 253 ALA B 270 1 18 HELIX 36 AD9 THR B 271 SER B 274 5 4 HELIX 37 AE1 LYS B 275 THR B 289 1 15 HELIX 38 AE2 ASN B 302 LEU B 319 1 18 HELIX 39 AE3 SER B 320 LYS B 324 5 5 HELIX 40 AE4 PRO B 325 ARG B 350 1 26 HELIX 41 AE5 ASP B 359 ALA B 363 5 5 HELIX 42 AE6 SER B 364 ILE B 376 1 13 HELIX 43 AE7 ILE B 376 VAL B 388 1 13 HELIX 44 AE8 ALA B 392 THR B 409 1 18 LINK NE2 HIS A 164 ZN ZN A 502 1555 1555 2.10 LINK NE2 HIS A 200 ZN ZN A 502 1555 1555 2.09 LINK OD2 ASP A 201 ZN ZN A 502 1555 1555 2.00 LINK OD1 ASP A 201 MG MG A 503 1555 1555 2.17 LINK OD1 ASP A 318 ZN ZN A 502 1555 1555 2.02 LINK ZN ZN A 502 O HOH A 620 1555 1555 2.08 LINK ZN ZN A 502 O HOH A 638 1555 1555 2.04 LINK MG MG A 503 O HOH A 628 1555 1555 2.08 LINK MG MG A 503 O HOH A 638 1555 1555 2.10 LINK MG MG A 503 O HOH A 641 1555 1555 2.08 LINK MG MG A 503 O HOH A 648 1555 1555 1.97 LINK MG MG A 503 O HOH A 668 1555 1555 2.21 LINK NE2 HIS B 164 ZN ZN B 503 1555 1555 2.10 LINK NE2 HIS B 200 ZN ZN B 503 1555 1555 2.09 LINK OD1 ASP B 201 MG MG B 502 1555 1555 2.17 LINK OD2 ASP B 201 ZN ZN B 503 1555 1555 2.00 LINK OD1 ASP B 318 ZN ZN B 503 1555 1555 2.00 LINK MG MG B 502 O HOH B 609 1555 1555 2.22 LINK MG MG B 502 O HOH B 614 1555 1555 2.14 LINK MG MG B 502 O HOH B 628 1555 1555 2.14 LINK MG MG B 502 O HOH B 634 1555 1555 1.96 LINK MG MG B 502 O HOH B 647 1555 1555 2.26 LINK ZN ZN B 503 O HOH B 610 1555 1555 2.22 LINK ZN ZN B 503 O HOH B 634 1555 1555 2.05 CISPEP 1 HIS A 389 PRO A 390 0 0.74 CISPEP 2 HIS B 389 PRO B 390 0 2.35 SITE 1 AC1 14 HIS A 160 SER A 208 MET A 273 HIS A 276 SITE 2 AC1 14 PHE A 340 GLN A 343 PRO A 356 MET A 357 SITE 3 AC1 14 CYS A 358 GLN A 369 PHE A 372 ILE A 376 SITE 4 AC1 14 HOH A 620 HOH A 628 SITE 1 AC2 6 HIS A 164 HIS A 200 ASP A 201 ASP A 318 SITE 2 AC2 6 HOH A 620 HOH A 638 SITE 1 AC3 6 ASP A 201 HOH A 628 HOH A 638 HOH A 641 SITE 2 AC3 6 HOH A 648 HOH A 668 SITE 1 AC4 14 HIS B 160 SER B 208 MET B 273 HIS B 276 SITE 2 AC4 14 PHE B 340 GLN B 343 PRO B 356 MET B 357 SITE 3 AC4 14 CYS B 358 GLN B 369 PHE B 372 ILE B 376 SITE 4 AC4 14 HOH B 610 HOH B 628 SITE 1 AC5 6 ASP B 201 HOH B 609 HOH B 614 HOH B 628 SITE 2 AC5 6 HOH B 634 HOH B 647 SITE 1 AC6 6 HIS B 164 HIS B 200 ASP B 201 ASP B 318 SITE 2 AC6 6 HOH B 610 HOH B 634 CRYST1 57.992 80.784 163.575 90.00 90.00 90.00 P 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 0.017244 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006113 0.00000