HEADER HYDROLASE/HYDROLASE INHIBITOR 14-JUL-17 5WH5 TITLE CRYSTAL STRUCTURE OF THE PDE4D2 CATALYTIC DOMAIN IN COMPLEX WITH TITLE 2 INHIBITOR (R)-ZL-N-91 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPDE3,PDE43; COMPND 5 EC: 3.1.4.53; COMPND 6 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET15B KEYWDS PHOSPHODIESTERASE, INHIBITORS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG REVDAT 3 13-MAR-24 5WH5 1 LINK REVDAT 2 31-JUL-19 5WH5 1 JRNL REVDAT 1 18-JUL-18 5WH5 0 JRNL AUTH X.FENG,H.WANG,M.YE,X.T.XU,Y.XU,W.YANG,H.T.ZHANG,G.SONG,H.KE JRNL TITL IDENTIFICATION OF A PDE4-SPECIFIC POCKET FOR THE DESIGN OF JRNL TITL 2 SELECTIVE INHIBITORS. JRNL REF BIOCHEMISTRY V. 57 4518 2018 JRNL REFN ISSN 0006-2960 JRNL PMID 29975048 JRNL DOI 10.1021/ACS.BIOCHEM.8B00336 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 65854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3389 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3163 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5270 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 388 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : 0.00000 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): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.721 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5437 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5156 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7372 ; 0.952 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11853 ; 0.744 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 4.369 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 272 ;33.117 ;25.147 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 957 ;11.495 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;11.835 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 850 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6099 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1235 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5WH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000228912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-08 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER AXIOM 200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69331 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 81.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE ~10MG/ML PDE4D2 (86-413) WAS REMARK 280 STORED IN A BUFFER OF 20 MM TRIS.BASE, PH 7.5, 50 MM NACL, 1 MM REMARK 280 2-MERCAPTOETHANOL, 1 MM EDTA AND MIXED WITH 2 MM (R)- OR (S)-5. REMARK 280 THEY WERE CRYSTALLIZED AT 4C BY HANGING DROP AGAINST A WELL REMARK 280 BUFFER OF 0.1 M HEPES PH 7.5, 15% PEG3350, 30% ETHYLENE GLYCOL, REMARK 280 AND 10% ISOPROPANOL., EVAPORATION, 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 29.73350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.72200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.94150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.72200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.73350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.94150 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 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 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 GLN A 412 REMARK 465 THR B 86 REMARK 465 GLU B 87 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 ASN A 362 74.02 -157.32 REMARK 500 ILE A 376 -60.18 -124.68 REMARK 500 SER B 294 51.11 35.62 REMARK 500 SER B 295 48.93 72.42 REMARK 500 ILE B 376 -58.90 -121.05 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 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 151 O REMARK 620 2 TYR A 153 O 92.4 REMARK 620 3 HOH A 712 O 99.1 84.8 REMARK 620 4 ASP B 301 OD1 94.9 50.1 133.3 REMARK 620 5 HOH B 611 O 82.1 171.6 89.8 136.4 REMARK 620 6 HOH B 673 O 86.1 89.5 172.5 40.2 96.4 REMARK 620 N 1 2 3 4 5 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 97.1 REMARK 620 3 ASP A 201 OD2 91.1 85.9 REMARK 620 4 ASP A 318 OD1 91.3 91.0 176.3 REMARK 620 5 HOH A 601 O 166.3 96.5 87.7 90.6 REMARK 620 6 HOH A 717 O 90.0 172.8 95.4 87.4 76.6 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 601 O 94.4 REMARK 620 3 HOH A 612 O 166.9 95.8 REMARK 620 4 HOH A 628 O 82.5 97.6 88.0 REMARK 620 5 HOH A 684 O 84.5 170.5 86.9 91.6 REMARK 620 6 HOH A 729 O 96.2 83.4 93.1 178.4 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 99.0 REMARK 620 3 ASP B 201 OD2 90.6 84.7 REMARK 620 4 ASP B 318 OD1 91.9 89.7 174.1 REMARK 620 5 HOH B 605 O 164.6 95.9 87.1 91.9 REMARK 620 6 HOH B 663 O 90.7 170.0 97.8 87.5 74.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 605 O 92.0 REMARK 620 3 HOH B 620 O 82.8 94.7 REMARK 620 4 HOH B 634 O 170.7 94.2 89.8 REMARK 620 5 HOH B 688 O 87.1 171.2 93.9 87.8 REMARK 620 6 HOH B 723 O 95.9 82.9 177.2 91.8 88.4 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 R91 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 MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue R91 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 503 DBREF 5WH5 A 86 412 UNP Q08499 PDE4D_HUMAN 252 578 DBREF 5WH5 B 86 412 UNP Q08499 PDE4D_HUMAN 252 578 SEQRES 1 A 327 THR GLU GLN GLU ASP VAL LEU ALA LYS GLU LEU GLU ASP SEQRES 2 A 327 VAL ASN LYS TRP GLY LEU HIS VAL PHE ARG ILE ALA GLU SEQRES 3 A 327 LEU SER GLY ASN ARG PRO LEU THR VAL ILE MET HIS THR SEQRES 4 A 327 ILE PHE GLN GLU ARG ASP LEU LEU LYS THR PHE LYS ILE SEQRES 5 A 327 PRO VAL ASP THR LEU ILE THR TYR LEU MET THR LEU GLU SEQRES 6 A 327 ASP HIS TYR HIS ALA ASP VAL ALA TYR HIS ASN ASN ILE SEQRES 7 A 327 HIS ALA ALA ASP VAL VAL GLN SER THR HIS VAL LEU LEU SEQRES 8 A 327 SER THR PRO ALA LEU GLU ALA VAL PHE THR ASP LEU GLU SEQRES 9 A 327 ILE LEU ALA ALA ILE PHE ALA SER ALA ILE HIS ASP VAL SEQRES 10 A 327 ASP HIS PRO GLY VAL SER ASN GLN PHE LEU ILE ASN THR SEQRES 11 A 327 ASN SER GLU LEU ALA LEU MET TYR ASN ASP SER SER VAL SEQRES 12 A 327 LEU GLU ASN HIS HIS LEU ALA VAL GLY PHE LYS LEU LEU SEQRES 13 A 327 GLN GLU GLU ASN CYS ASP ILE PHE GLN ASN LEU THR LYS SEQRES 14 A 327 LYS GLN ARG GLN SER LEU ARG LYS MET VAL ILE ASP ILE SEQRES 15 A 327 VAL LEU ALA THR ASP MET SER LYS HIS MET ASN LEU LEU SEQRES 16 A 327 ALA ASP LEU LYS THR MET VAL GLU THR LYS LYS VAL THR SEQRES 17 A 327 SER SER GLY VAL LEU LEU LEU ASP ASN TYR SER ASP ARG SEQRES 18 A 327 ILE GLN VAL LEU GLN ASN MET VAL HIS CYS ALA ASP LEU SEQRES 19 A 327 SER ASN PRO THR LYS PRO LEU GLN LEU TYR ARG GLN TRP SEQRES 20 A 327 THR ASP ARG ILE MET GLU GLU PHE PHE ARG GLN GLY ASP SEQRES 21 A 327 ARG GLU ARG GLU ARG GLY MET GLU ILE SER PRO MET CYS SEQRES 22 A 327 ASP LYS HIS ASN ALA SER VAL GLU LYS SER GLN VAL GLY SEQRES 23 A 327 PHE ILE ASP TYR ILE VAL HIS PRO LEU TRP GLU THR TRP SEQRES 24 A 327 ALA ASP LEU VAL HIS PRO ASP ALA GLN ASP ILE LEU ASP SEQRES 25 A 327 THR LEU GLU ASP ASN ARG GLU TRP TYR GLN SER THR ILE SEQRES 26 A 327 PRO GLN SEQRES 1 B 327 THR GLU GLN GLU ASP VAL LEU ALA LYS GLU LEU GLU ASP SEQRES 2 B 327 VAL ASN LYS TRP GLY LEU HIS VAL PHE ARG ILE ALA GLU SEQRES 3 B 327 LEU SER GLY ASN ARG PRO LEU THR VAL ILE MET HIS THR SEQRES 4 B 327 ILE PHE GLN GLU ARG ASP LEU LEU LYS THR PHE LYS ILE SEQRES 5 B 327 PRO VAL ASP THR LEU ILE THR TYR LEU MET THR LEU GLU SEQRES 6 B 327 ASP HIS TYR HIS ALA ASP VAL ALA TYR HIS ASN ASN ILE SEQRES 7 B 327 HIS ALA ALA ASP VAL VAL GLN SER THR HIS VAL LEU LEU SEQRES 8 B 327 SER THR PRO ALA LEU GLU ALA VAL PHE THR ASP LEU GLU SEQRES 9 B 327 ILE LEU ALA ALA ILE PHE ALA SER ALA ILE HIS ASP VAL SEQRES 10 B 327 ASP HIS PRO GLY VAL SER ASN GLN PHE LEU ILE ASN THR SEQRES 11 B 327 ASN SER GLU LEU ALA LEU MET TYR ASN ASP SER SER VAL SEQRES 12 B 327 LEU GLU ASN HIS HIS LEU ALA VAL GLY PHE LYS LEU LEU SEQRES 13 B 327 GLN GLU GLU ASN CYS ASP ILE PHE GLN ASN LEU THR LYS SEQRES 14 B 327 LYS GLN ARG GLN SER LEU ARG LYS MET VAL ILE ASP ILE SEQRES 15 B 327 VAL LEU ALA THR ASP MET SER LYS HIS MET ASN LEU LEU SEQRES 16 B 327 ALA ASP LEU LYS THR MET VAL GLU THR LYS LYS VAL THR SEQRES 17 B 327 SER SER GLY VAL LEU LEU LEU ASP ASN TYR SER ASP ARG SEQRES 18 B 327 ILE GLN VAL LEU GLN ASN MET VAL HIS CYS ALA ASP LEU SEQRES 19 B 327 SER ASN PRO THR LYS PRO LEU GLN LEU TYR ARG GLN TRP SEQRES 20 B 327 THR ASP ARG ILE MET GLU GLU PHE PHE ARG GLN GLY ASP SEQRES 21 B 327 ARG GLU ARG GLU ARG GLY MET GLU ILE SER PRO MET CYS SEQRES 22 B 327 ASP LYS HIS ASN ALA SER VAL GLU LYS SER GLN VAL GLY SEQRES 23 B 327 PHE ILE ASP TYR ILE VAL HIS PRO LEU TRP GLU THR TRP SEQRES 24 B 327 ALA ASP LEU VAL HIS PRO ASP ALA GLN ASP ILE LEU ASP SEQRES 25 B 327 THR LEU GLU ASP ASN ARG GLU TRP TYR GLN SER THR ILE SEQRES 26 B 327 PRO GLN HET R91 A 501 22 HET ZN A 502 1 HET MG A 503 1 HET MG A 504 1 HET R91 B 501 22 HET ZN B 502 1 HET MG B 503 1 HETNAM R91 1-[4-(DIFLUOROMETHOXY)-3-{[(3R)-OXOLAN-3- HETNAM 2 R91 YL]OXY}PHENYL]-3-METHYLBUTAN-1-ONE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 3 R91 2(C16 H20 F2 O4) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 MG 3(MG 2+) FORMUL 10 HOH *388(H2 O) HELIX 1 AA1 THR A 86 GLU A 97 1 12 HELIX 2 AA2 HIS A 105 SER A 113 1 9 HELIX 3 AA3 ARG A 116 ARG A 129 1 14 HELIX 4 AA4 ASP A 130 PHE A 135 1 6 HELIX 5 AA5 PRO A 138 HIS A 152 1 15 HELIX 6 AA6 ASN A 161 SER A 177 1 17 HELIX 7 AA7 THR A 178 GLU A 182 5 5 HELIX 8 AA8 THR A 186 HIS A 200 1 15 HELIX 9 AA9 SER A 208 THR A 215 1 8 HELIX 10 AB1 SER A 217 ASN A 224 1 8 HELIX 11 AB2 SER A 227 LEU A 240 1 14 HELIX 12 AB3 LEU A 241 GLU A 243 5 3 HELIX 13 AB4 THR A 253 ALA A 270 1 18 HELIX 14 AB5 THR A 271 SER A 274 5 4 HELIX 15 AB6 LYS A 275 THR A 289 1 15 HELIX 16 AB7 ASN A 302 LEU A 319 1 18 HELIX 17 AB8 SER A 320 LYS A 324 5 5 HELIX 18 AB9 PRO A 325 GLY A 351 1 27 HELIX 19 AC1 SER A 364 ILE A 376 1 13 HELIX 20 AC2 ILE A 376 VAL A 388 1 13 HELIX 21 AC3 ALA A 392 THR A 409 1 18 HELIX 22 AC4 GLU B 89 LEU B 96 1 8 HELIX 23 AC5 GLU B 97 VAL B 99 5 3 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ARG B 129 1 14 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 GLY B 351 1 27 HELIX 41 AE5 SER B 364 ILE B 376 1 13 HELIX 42 AE6 ILE B 376 VAL B 388 1 13 HELIX 43 AE7 ALA B 392 THR B 409 1 18 SHEET 1 AA1 2 VAL B 292 THR B 293 0 SHEET 2 AA1 2 VAL B 297 LEU B 298 -1 O VAL B 297 N THR B 293 LINK O ASP A 151 MG MG A 504 1555 1555 2.17 LINK O TYR A 153 MG MG A 504 1555 1555 2.18 LINK NE2 HIS A 164 ZN ZN A 502 1555 1555 2.14 LINK NE2 HIS A 200 ZN ZN A 502 1555 1555 2.16 LINK OD2 ASP A 201 ZN ZN A 502 1555 1555 2.03 LINK OD1 ASP A 201 MG MG A 503 1555 1555 2.17 LINK OD1 ASP A 318 ZN ZN A 502 1555 1555 2.06 LINK ZN ZN A 502 O HOH A 601 1555 1555 2.32 LINK ZN ZN A 502 O HOH A 717 1555 1555 2.18 LINK MG MG A 503 O HOH A 601 1555 1555 2.07 LINK MG MG A 503 O HOH A 612 1555 1555 2.13 LINK MG MG A 503 O HOH A 628 1555 1555 2.11 LINK MG MG A 503 O HOH A 684 1555 1555 2.21 LINK MG MG A 503 O HOH A 729 1555 1555 2.13 LINK MG MG A 504 O HOH A 712 1555 1555 2.05 LINK MG MG A 504 OD1 ASP B 301 3545 1555 2.20 LINK MG MG A 504 O HOH B 611 1555 3555 2.18 LINK MG MG A 504 O HOH B 673 1555 3555 2.24 LINK NE2 HIS B 164 ZN ZN B 502 1555 1555 2.14 LINK NE2 HIS B 200 ZN ZN B 502 1555 1555 2.16 LINK OD2 ASP B 201 ZN ZN B 502 1555 1555 2.04 LINK OD1 ASP B 201 MG MG B 503 1555 1555 2.17 LINK OD1 ASP B 318 ZN ZN B 502 1555 1555 2.06 LINK ZN ZN B 502 O HOH B 605 1555 1555 2.33 LINK ZN ZN B 502 O HOH B 663 1555 1555 2.25 LINK MG MG B 503 O HOH B 605 1555 1555 2.07 LINK MG MG B 503 O HOH B 620 1555 1555 2.09 LINK MG MG B 503 O HOH B 634 1555 1555 2.10 LINK MG MG B 503 O HOH B 688 1555 1555 2.17 LINK MG MG B 503 O HOH B 723 1555 1555 2.11 CISPEP 1 HIS A 389 PRO A 390 0 2.44 CISPEP 2 HIS B 389 PRO B 390 0 -0.09 SITE 1 AC1 10 TYR A 159 ASN A 321 TYR A 329 TRP A 332 SITE 2 AC1 10 THR A 333 ILE A 336 MET A 357 SER A 368 SITE 3 AC1 10 GLN A 369 PHE A 372 SITE 1 AC2 6 HIS A 164 HIS A 200 ASP A 201 ASP A 318 SITE 2 AC2 6 HOH A 601 HOH A 717 SITE 1 AC3 6 ASP A 201 HOH A 601 HOH A 612 HOH A 628 SITE 2 AC3 6 HOH A 684 HOH A 729 SITE 1 AC4 6 ASP A 151 TYR A 153 HOH A 712 ASP B 301 SITE 2 AC4 6 HOH B 611 HOH B 673 SITE 1 AC5 14 TYR B 159 ASP B 318 LEU B 319 ASN B 321 SITE 2 AC5 14 PRO B 322 TYR B 329 TRP B 332 THR B 333 SITE 3 AC5 14 ILE B 336 MET B 357 SER B 368 GLN B 369 SITE 4 AC5 14 PHE B 372 HOH B 697 SITE 1 AC6 6 HIS B 164 HIS B 200 ASP B 201 ASP B 318 SITE 2 AC6 6 HOH B 605 HOH B 663 SITE 1 AC7 6 ASP B 201 HOH B 605 HOH B 620 HOH B 634 SITE 2 AC7 6 HOH B 688 HOH B 723 CRYST1 59.467 79.883 163.444 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 0.016816 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006118 0.00000