HEADER HYDROLASE 13-DEC-17 6F8W TITLE CRYSTAL STRUCTURE OF THE PDE4D CATALYTIC DOMAIN IN COMPLEX WITH GEBR- TITLE 2 18A 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PDE4, CATALYTIC DOMAIN, INHIBITOR, GEBR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PROSDOCIMI,S.DONINI,E.PARISINI REVDAT 3 17-JAN-24 6F8W 1 LINK REVDAT 2 23-MAY-18 6F8W 1 JRNL REVDAT 1 16-MAY-18 6F8W 0 JRNL AUTH T.PROSDOCIMI,L.MOLLICA,S.DONINI,M.S.SEMRAU,A.P.LUCARELLI, JRNL AUTH 2 E.AIOLFI,A.CAVALLI,P.STORICI,S.ALFEI,C.BRULLO,O.BRUNO, JRNL AUTH 3 E.PARISINI JRNL TITL MOLECULAR BASES OF PDE4D INHIBITION BY MEMORY-ENHANCING GEBR JRNL TITL 2 LIBRARY COMPOUNDS. JRNL REF BIOCHEMISTRY V. 57 2876 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29652483 JRNL DOI 10.1021/ACS.BIOCHEM.8B00288 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 196940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9853 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7082 - 4.9713 1.00 6237 329 0.1635 0.1917 REMARK 3 2 4.9713 - 3.9465 0.99 6224 325 0.1475 0.1598 REMARK 3 3 3.9465 - 3.4479 0.99 6214 329 0.1733 0.1891 REMARK 3 4 3.4479 - 3.1327 0.99 6226 332 0.1832 0.2020 REMARK 3 5 3.1327 - 2.9082 1.00 6251 321 0.1923 0.2089 REMARK 3 6 2.9082 - 2.7368 1.00 6246 333 0.1944 0.2312 REMARK 3 7 2.7368 - 2.5997 0.99 6203 333 0.1896 0.2199 REMARK 3 8 2.5997 - 2.4866 0.99 6197 331 0.1884 0.2305 REMARK 3 9 2.4866 - 2.3908 0.99 6238 331 0.1895 0.2112 REMARK 3 10 2.3908 - 2.3083 0.99 6250 327 0.1869 0.2123 REMARK 3 11 2.3083 - 2.2362 0.99 6199 320 0.1925 0.2401 REMARK 3 12 2.2362 - 2.1723 1.00 6252 332 0.1872 0.2333 REMARK 3 13 2.1723 - 2.1151 1.00 6239 335 0.1870 0.2224 REMARK 3 14 2.1151 - 2.0635 0.99 6275 332 0.1905 0.2145 REMARK 3 15 2.0635 - 2.0166 1.00 6225 327 0.1972 0.2416 REMARK 3 16 2.0166 - 1.9736 1.00 6241 328 0.2019 0.2467 REMARK 3 17 1.9736 - 1.9342 1.00 6292 328 0.2172 0.2670 REMARK 3 18 1.9342 - 1.8977 1.00 6216 329 0.2350 0.2931 REMARK 3 19 1.8977 - 1.8638 1.00 6273 328 0.2346 0.2587 REMARK 3 20 1.8638 - 1.8322 1.00 6269 326 0.2271 0.2874 REMARK 3 21 1.8322 - 1.8026 0.99 6205 327 0.2344 0.2888 REMARK 3 22 1.8026 - 1.7749 0.99 6257 326 0.2376 0.2518 REMARK 3 23 1.7749 - 1.7488 1.00 6250 330 0.2415 0.2784 REMARK 3 24 1.7488 - 1.7241 1.00 6216 319 0.2504 0.2893 REMARK 3 25 1.7241 - 1.7008 1.00 6257 332 0.2714 0.2994 REMARK 3 26 1.7008 - 1.6788 1.00 6271 331 0.2768 0.3206 REMARK 3 27 1.6788 - 1.6578 1.00 6234 327 0.2848 0.2911 REMARK 3 28 1.6578 - 1.6378 1.00 6271 332 0.2977 0.3325 REMARK 3 29 1.6378 - 1.6188 1.00 6273 331 0.3098 0.3429 REMARK 3 30 1.6188 - 1.6006 0.97 6086 322 0.3200 0.3609 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 5555 REMARK 3 ANGLE : 0.928 7569 REMARK 3 CHIRALITY : 0.037 864 REMARK 3 PLANARITY : 0.005 970 REMARK 3 DIHEDRAL : 14.403 2082 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6F8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 196940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 45.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 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: NULL REMARK 200 STARTING MODEL: 6F6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PEG 3350 MAGNESIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 32.51950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.38250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.35850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.38250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.51950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.35850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 243 REMARK 465 SER A 244 REMARK 465 ILE A 245 REMARK 465 PRO A 246 REMARK 465 ARG A 247 REMARK 465 PHE A 248 REMARK 465 GLY A 249 REMARK 465 VAL A 250 REMARK 465 LYS A 251 REMARK 465 THR A 252 REMARK 465 GLU A 253 REMARK 465 GLN A 254 REMARK 465 GLU A 255 REMARK 465 ASP A 256 REMARK 465 VAL A 257 REMARK 465 HIS A 580 REMARK 465 HIS A 581 REMARK 465 HIS A 582 REMARK 465 HIS A 583 REMARK 465 HIS A 584 REMARK 465 HIS A 585 REMARK 465 MET B 243 REMARK 465 SER B 244 REMARK 465 ILE B 245 REMARK 465 PRO B 246 REMARK 465 GLN B 578 REMARK 465 ALA B 579 REMARK 465 HIS B 580 REMARK 465 HIS B 581 REMARK 465 HIS B 582 REMARK 465 HIS B 583 REMARK 465 HIS B 584 REMARK 465 HIS B 585 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 B 247 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 251 CG CD CE NZ REMARK 470 THR B 252 OG1 CG2 REMARK 470 GLU B 253 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 701 O HOH B 853 1.92 REMARK 500 O HOH B 770 O HOH B 920 1.93 REMARK 500 O HOH A 701 O HOH A 850 1.94 REMARK 500 O HOH B 701 O HOH B 890 1.99 REMARK 500 NE2 HIS A 326 O HOH A 701 2.00 REMARK 500 O HOH B 920 O HOH B 934 2.02 REMARK 500 NE2 HIS B 326 O HOH B 701 2.04 REMARK 500 O HOH A 819 O HOH A 919 2.08 REMARK 500 O HOH A 701 O HOH A 872 2.08 REMARK 500 NZ LYS B 428 O HOH B 702 2.11 REMARK 500 OE2 GLU B 504 NH2 ARG B 508 2.11 REMARK 500 OD1 ASP B 511 NH2 ARG B 514 2.14 REMARK 500 NH2 ARG A 274 O HOH A 702 2.15 REMARK 500 OD1 ASP A 511 NH2 ARG A 514 2.16 REMARK 500 NE2 GLN A 408 O HOH A 703 2.17 REMARK 500 O HOH A 941 O HOH A 942 2.18 REMARK 500 NH1 ARG A 423 O HOH A 704 2.18 REMARK 500 O HOH A 702 O HOH A 912 2.18 REMARK 500 O HOH B 794 O HOH B 867 2.19 REMARK 500 O HOH B 924 O HOH B 934 2.19 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 ASN A 327 -169.23 -125.04 REMARK 500 ILE A 542 -59.00 -126.39 REMARK 500 VAL B 250 -11.31 -143.11 REMARK 500 LYS B 251 113.71 67.30 REMARK 500 GLN B 254 -89.34 -88.85 REMARK 500 GLU B 255 -57.38 154.97 REMARK 500 ILE B 542 -59.71 -120.65 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 330 NE2 REMARK 620 2 HIS A 366 NE2 95.4 REMARK 620 3 ASP A 367 OD2 90.5 84.8 REMARK 620 4 ASP A 484 OD1 86.8 90.3 174.2 REMARK 620 5 HOH A 749 O 169.9 94.7 91.2 92.3 REMARK 620 6 HOH A 850 O 86.0 175.4 99.6 85.4 83.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 367 OD1 REMARK 620 2 HOH A 749 O 94.2 REMARK 620 3 HOH A 781 O 85.2 95.5 REMARK 620 4 HOH A 793 O 168.2 92.9 84.7 REMARK 620 5 HOH A 813 O 88.7 174.1 89.9 85.2 REMARK 620 6 HOH A 872 O 100.0 87.6 173.8 89.7 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 764 O REMARK 620 2 HOH A 765 O 81.5 REMARK 620 3 HOH A 878 O 81.6 147.6 REMARK 620 4 HOH A 901 O 93.6 64.3 89.5 REMARK 620 5 HOH B 769 O 167.8 106.8 86.8 82.5 REMARK 620 6 HOH B 914 O 84.7 119.2 86.4 175.8 98.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 724 O REMARK 620 2 HOH A 760 O 82.3 REMARK 620 3 HOH A 939 O 101.8 86.7 REMARK 620 4 HOH B 725 O 86.4 91.6 171.4 REMARK 620 5 HOH B 798 O 169.9 96.5 88.2 83.6 REMARK 620 6 HOH B 944 O 90.3 162.7 79.5 103.6 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 330 NE2 REMARK 620 2 HIS B 366 NE2 96.3 REMARK 620 3 ASP B 367 OD2 89.4 85.6 REMARK 620 4 ASP B 484 OD1 88.9 89.9 175.0 REMARK 620 5 HOH B 749 O 169.4 94.1 89.4 93.2 REMARK 620 6 HOH B 853 O 86.2 176.8 96.5 88.0 83.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 367 OD1 REMARK 620 2 HOH B 749 O 94.9 REMARK 620 3 HOH B 774 O 168.1 92.5 REMARK 620 4 HOH B 799 O 85.0 94.8 85.2 REMARK 620 5 HOH B 824 O 87.5 173.6 86.1 91.3 REMARK 620 6 HOH B 890 O 100.7 88.6 88.7 173.1 85.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 467 OD2 REMARK 620 2 ASP B 471 OD2 97.9 REMARK 620 3 HOH B 771 O 171.6 85.1 REMARK 620 4 HOH B 776 O 82.1 91.4 90.1 REMARK 620 5 HOH B 790 O 101.3 83.7 86.8 174.3 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D0E A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D0E B 604 DBREF 6F8W A 244 578 UNP Q08499 PDE4D_HUMAN 244 578 DBREF 6F8W B 244 578 UNP Q08499 PDE4D_HUMAN 244 578 SEQADV 6F8W MET A 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F8W ALA A 579 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS A 580 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS A 581 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS A 582 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS A 583 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS A 584 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS A 585 UNP Q08499 EXPRESSION TAG SEQADV 6F8W MET B 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F8W ALA B 579 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS B 580 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS B 581 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS B 582 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS B 583 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS B 584 UNP Q08499 EXPRESSION TAG SEQADV 6F8W HIS B 585 UNP Q08499 EXPRESSION TAG SEQRES 1 A 343 MET SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU SEQRES 2 A 343 ASP VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP SEQRES 3 A 343 GLY LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN SEQRES 4 A 343 ARG PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU SEQRES 5 A 343 ARG ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR SEQRES 6 A 343 LEU ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS SEQRES 7 A 343 ALA ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP SEQRES 8 A 343 VAL VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 9 A 343 LEU GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 10 A 343 ILE PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 11 A 343 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 12 A 343 ALA LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS SEQRES 13 A 343 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN SEQRES 14 A 343 CYS ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SEQRES 15 A 343 SER LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR SEQRES 16 A 343 ASP MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS SEQRES 17 A 343 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 18 A 343 LEU LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU SEQRES 19 A 343 GLN ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 20 A 343 LYS PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 21 A 343 MET GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU SEQRES 22 A 343 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN SEQRES 23 A 343 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 24 A 343 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 25 A 343 HIS PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 26 A 343 ASN ARG GLU TRP TYR GLN SER THR ILE PRO GLN ALA HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS SEQRES 1 B 343 MET SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU SEQRES 2 B 343 ASP VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP SEQRES 3 B 343 GLY LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN SEQRES 4 B 343 ARG PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU SEQRES 5 B 343 ARG ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR SEQRES 6 B 343 LEU ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS SEQRES 7 B 343 ALA ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP SEQRES 8 B 343 VAL VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 9 B 343 LEU GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 10 B 343 ILE PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 11 B 343 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 12 B 343 ALA LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS SEQRES 13 B 343 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN SEQRES 14 B 343 CYS ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SEQRES 15 B 343 SER LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR SEQRES 16 B 343 ASP MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS SEQRES 17 B 343 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 18 B 343 LEU LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU SEQRES 19 B 343 GLN ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 20 B 343 LYS PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 21 B 343 MET GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU SEQRES 22 B 343 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN SEQRES 23 B 343 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 24 B 343 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 25 B 343 HIS PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 26 B 343 ASN ARG GLU TRP TYR GLN SER THR ILE PRO GLN ALA HIS SEQRES 27 B 343 HIS HIS HIS HIS HIS HET ZN A 601 1 HET MG A 602 1 HET MG A 603 1 HET MG A 604 1 HET D0E A 605 58 HET ZN B 601 1 HET MG B 602 1 HET MG B 603 1 HET D0E B 604 58 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM D0E 3-[3-(3-CYCLOPENTYLOXY-4-METHOXY-PHENYL)PYRAZOL-1-YL]- HETNAM 2 D0E 1-MORPHOLIN-4-YL-PROPAN-1-ONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 5(MG 2+) FORMUL 7 D0E 2(C22 H29 N3 O4) FORMUL 12 HOH *492(H2 O) HELIX 1 AA1 LYS A 260 VAL A 265 5 6 HELIX 2 AA2 HIS A 271 SER A 279 1 9 HELIX 3 AA3 ARG A 282 ARG A 295 1 14 HELIX 4 AA4 ASP A 296 PHE A 301 1 6 HELIX 5 AA5 PRO A 304 HIS A 318 1 15 HELIX 6 AA6 ASN A 327 SER A 343 1 17 HELIX 7 AA7 THR A 344 GLU A 348 5 5 HELIX 8 AA8 THR A 352 HIS A 366 1 15 HELIX 9 AA9 SER A 374 THR A 381 1 8 HELIX 10 AB1 SER A 383 ASN A 390 1 8 HELIX 11 AB2 SER A 393 LEU A 406 1 14 HELIX 12 AB3 LEU A 407 GLU A 409 5 3 HELIX 13 AB4 THR A 419 ALA A 436 1 18 HELIX 14 AB5 THR A 437 SER A 440 5 4 HELIX 15 AB6 LYS A 441 THR A 455 1 15 HELIX 16 AB7 ASN A 468 LEU A 485 1 18 HELIX 17 AB8 SER A 486 LYS A 490 5 5 HELIX 18 AB9 PRO A 491 ARG A 516 1 26 HELIX 19 AC1 SER A 530 ILE A 542 1 13 HELIX 20 AC2 ILE A 542 VAL A 554 1 13 HELIX 21 AC3 ALA A 558 SER A 574 1 17 HELIX 22 AC4 GLU B 255 GLU B 263 1 9 HELIX 23 AC5 HIS B 271 SER B 279 1 9 HELIX 24 AC6 ARG B 282 ARG B 295 1 14 HELIX 25 AC7 ASP B 296 LYS B 302 1 7 HELIX 26 AC8 PRO B 304 HIS B 318 1 15 HELIX 27 AC9 ASN B 327 SER B 343 1 17 HELIX 28 AD1 THR B 344 GLU B 348 5 5 HELIX 29 AD2 THR B 352 HIS B 366 1 15 HELIX 30 AD3 SER B 374 THR B 381 1 8 HELIX 31 AD4 SER B 383 TYR B 389 1 7 HELIX 32 AD5 SER B 393 LEU B 406 1 14 HELIX 33 AD6 LEU B 407 GLU B 409 5 3 HELIX 34 AD7 THR B 419 ALA B 436 1 18 HELIX 35 AD8 THR B 437 SER B 440 5 4 HELIX 36 AD9 LYS B 441 THR B 455 1 15 HELIX 37 AE1 ASN B 468 LEU B 485 1 18 HELIX 38 AE2 SER B 486 LYS B 490 5 5 HELIX 39 AE3 PRO B 491 ARG B 516 1 26 HELIX 40 AE4 SER B 530 ILE B 542 1 13 HELIX 41 AE5 ILE B 542 VAL B 554 1 13 HELIX 42 AE6 ALA B 558 THR B 575 1 18 LINK NE2 HIS A 330 ZN ZN A 601 1555 1555 2.17 LINK NE2 HIS A 366 ZN ZN A 601 1555 1555 2.17 LINK OD2 ASP A 367 ZN ZN A 601 1555 1555 2.06 LINK OD1 ASP A 367 MG MG A 602 1555 1555 2.06 LINK OD1 ASP A 484 ZN ZN A 601 1555 1555 2.17 LINK ZN ZN A 601 O HOH A 749 1555 1555 2.19 LINK ZN ZN A 601 O HOH A 850 1555 1555 2.12 LINK MG MG A 602 O HOH A 749 1555 1555 2.07 LINK MG MG A 602 O HOH A 781 1555 1555 2.15 LINK MG MG A 602 O HOH A 793 1555 1555 2.06 LINK MG MG A 602 O HOH A 813 1555 1555 2.18 LINK MG MG A 602 O HOH A 872 1555 1555 2.09 LINK MG MG A 603 O HOH A 764 1555 1555 2.15 LINK MG MG A 603 O HOH A 765 1555 1555 2.24 LINK MG MG A 603 O HOH A 878 1555 1555 2.61 LINK MG MG A 603 O HOH A 901 1555 1555 2.50 LINK MG MG A 603 O HOH B 769 1555 3544 2.05 LINK MG MG A 603 O HOH B 914 1555 3544 2.06 LINK MG MG A 604 O HOH A 724 1555 1555 2.33 LINK MG MG A 604 O HOH A 760 1555 1555 2.17 LINK MG MG A 604 O HOH A 939 1555 1555 2.26 LINK MG MG A 604 O HOH B 725 1555 2455 2.21 LINK MG MG A 604 O HOH B 798 1555 2455 2.04 LINK MG MG A 604 O HOH B 944 1555 2455 2.23 LINK NE2 HIS B 330 ZN ZN B 601 1555 1555 2.19 LINK NE2 HIS B 366 ZN ZN B 601 1555 1555 2.17 LINK OD2 ASP B 367 ZN ZN B 601 1555 1555 2.07 LINK OD1 ASP B 367 MG MG B 602 1555 1555 2.06 LINK OD2 ASP B 467 MG MG B 603 1555 1555 2.05 LINK OD2 ASP B 471 MG MG B 603 1555 1555 2.11 LINK OD1 ASP B 484 ZN ZN B 601 1555 1555 2.16 LINK ZN ZN B 601 O HOH B 749 1555 1555 2.22 LINK ZN ZN B 601 O HOH B 853 1555 1555 2.11 LINK MG MG B 602 O HOH B 749 1555 1555 2.01 LINK MG MG B 602 O HOH B 774 1555 1555 2.23 LINK MG MG B 602 O HOH B 799 1555 1555 2.11 LINK MG MG B 602 O HOH B 824 1555 1555 2.17 LINK MG MG B 602 O HOH B 890 1555 1555 2.11 LINK MG MG B 603 O HOH B 771 1555 1555 2.14 LINK MG MG B 603 O HOH B 776 1555 1555 2.08 LINK MG MG B 603 O HOH B 790 1555 1555 1.97 CISPEP 1 HIS A 555 PRO A 556 0 2.66 CISPEP 2 GLU B 253 GLN B 254 0 10.46 CISPEP 3 HIS B 555 PRO B 556 0 2.33 SITE 1 AC1 6 HIS A 330 HIS A 366 ASP A 367 ASP A 484 SITE 2 AC1 6 HOH A 749 HOH A 850 SITE 1 AC2 6 ASP A 367 HOH A 749 HOH A 781 HOH A 793 SITE 2 AC2 6 HOH A 813 HOH A 872 SITE 1 AC3 6 HOH A 764 HOH A 765 HOH A 878 HOH A 901 SITE 2 AC3 6 HOH B 769 HOH B 914 SITE 1 AC4 6 HOH A 724 HOH A 760 HOH A 939 HOH B 725 SITE 2 AC4 6 HOH B 798 HOH B 944 SITE 1 AC5 19 TYR A 325 THR A 437 MET A 439 ASP A 484 SITE 2 AC5 19 LEU A 485 ASN A 487 THR A 499 ILE A 502 SITE 3 AC5 19 MET A 503 PHE A 506 MET A 523 SER A 534 SITE 4 AC5 19 GLN A 535 PHE A 538 HOH A 701 HOH A 793 SITE 5 AC5 19 HOH A 794 HOH A 802 HOH A 831 SITE 1 AC6 6 HIS B 330 HIS B 366 ASP B 367 ASP B 484 SITE 2 AC6 6 HOH B 749 HOH B 853 SITE 1 AC7 6 ASP B 367 HOH B 749 HOH B 774 HOH B 799 SITE 2 AC7 6 HOH B 824 HOH B 890 SITE 1 AC8 6 ASP B 467 ASP B 471 HIS B 527 HOH B 771 SITE 2 AC8 6 HOH B 776 HOH B 790 SITE 1 AC9 17 THR B 437 MET B 439 ASP B 484 LEU B 485 SITE 2 AC9 17 ASN B 487 THR B 499 ILE B 502 MET B 503 SITE 3 AC9 17 PHE B 506 MET B 523 GLN B 535 PHE B 538 SITE 4 AC9 17 HOH B 701 HOH B 774 HOH B 787 HOH B 804 SITE 5 AC9 17 HOH B 889 CRYST1 65.039 98.717 120.765 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 0.015375 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010130 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008281 0.00000