HEADER HYDROLASE 22-DEC-17 6FDC TITLE CRYSTAL STRUCTURE OF THE PDE4D CATALYTIC DOMAIN IN COMPLEX WITH GEBR- TITLE 2 32A 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 2 23-MAY-18 6FDC 1 JRNL REVDAT 1 16-MAY-18 6FDC 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. 1.45 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 263295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 13176 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 49.3523 - 4.5044 1.00 8331 450 0.1545 0.1769 REMARK 3 2 4.5044 - 3.5756 1.00 8324 434 0.1505 0.1723 REMARK 3 3 3.5756 - 3.1237 1.00 8371 435 0.1715 0.1968 REMARK 3 4 3.1237 - 2.8381 1.00 8349 441 0.1786 0.2047 REMARK 3 5 2.8381 - 2.6347 1.00 8307 434 0.1776 0.1941 REMARK 3 6 2.6347 - 2.4794 1.00 8343 433 0.1748 0.2061 REMARK 3 7 2.4794 - 2.3552 1.00 8329 443 0.1783 0.1915 REMARK 3 8 2.3552 - 2.2527 1.00 8353 441 0.1735 0.1904 REMARK 3 9 2.2527 - 2.1660 1.00 8350 440 0.1724 0.1909 REMARK 3 10 2.1660 - 2.0912 1.00 8318 441 0.1788 0.1877 REMARK 3 11 2.0912 - 2.0258 1.00 8314 438 0.1807 0.2053 REMARK 3 12 2.0258 - 1.9679 1.00 8345 439 0.1847 0.2011 REMARK 3 13 1.9679 - 1.9161 1.00 8357 447 0.1885 0.2127 REMARK 3 14 1.9161 - 1.8694 1.00 8288 437 0.1898 0.2201 REMARK 3 15 1.8694 - 1.8269 1.00 8378 445 0.1932 0.1999 REMARK 3 16 1.8269 - 1.7880 1.00 8267 432 0.1884 0.2372 REMARK 3 17 1.7880 - 1.7522 1.00 8386 442 0.1936 0.2022 REMARK 3 18 1.7522 - 1.7192 1.00 8396 445 0.1892 0.2272 REMARK 3 19 1.7192 - 1.6885 1.00 8297 435 0.1911 0.2029 REMARK 3 20 1.6885 - 1.6598 1.00 8334 437 0.1969 0.2048 REMARK 3 21 1.6598 - 1.6331 1.00 8370 433 0.1999 0.2206 REMARK 3 22 1.6331 - 1.6079 1.00 8328 441 0.1967 0.2303 REMARK 3 23 1.6079 - 1.5843 1.00 8329 438 0.2080 0.2379 REMARK 3 24 1.5843 - 1.5620 1.00 8367 439 0.2142 0.2258 REMARK 3 25 1.5620 - 1.5409 1.00 8290 439 0.2182 0.2332 REMARK 3 26 1.5409 - 1.5208 1.00 8332 443 0.2273 0.2291 REMARK 3 27 1.5208 - 1.5018 1.00 8347 442 0.2338 0.2357 REMARK 3 28 1.5018 - 1.4837 1.00 8375 442 0.2428 0.2462 REMARK 3 29 1.4837 - 1.4665 1.00 8266 436 0.2545 0.2730 REMARK 3 30 1.4665 - 1.4500 1.00 8378 434 0.2644 0.2926 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.510 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 5543 REMARK 3 ANGLE : 1.038 7549 REMARK 3 CHIRALITY : 0.065 867 REMARK 3 PLANARITY : 0.005 965 REMARK 3 DIHEDRAL : 14.058 2074 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 6FDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007798. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 263295 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 49.324 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 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 32.34600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.08250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.30400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.08250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.34600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.30400 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: 2590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 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 GLN A 578 REMARK 465 ALA A 579 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 ARG B 247 REMARK 465 PHE B 248 REMARK 465 GLY B 249 REMARK 465 VAL B 250 REMARK 465 LYS B 251 REMARK 465 THR B 252 REMARK 465 GLU B 253 REMARK 465 GLN B 254 REMARK 465 GLU B 255 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 LYS A 251 CG CD CE NZ REMARK 470 GLN A 254 CG CD OE1 NE2 REMARK 470 GLU A 255 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 A 701 O HOH A 839 1.89 REMARK 500 O HOH B 705 O HOH B 838 1.92 REMARK 500 O HOH A 701 O HOH A 895 2.02 REMARK 500 O HOH B 705 O HOH B 871 2.04 REMARK 500 OD1 ASP A 511 NH2 ARG A 514 2.08 REMARK 500 NE2 HIS A 326 O HOH A 701 2.11 REMARK 500 OD1 ASP B 511 NH2 ARG B 514 2.13 REMARK 500 OG SER B 534 O HOH B 701 2.17 REMARK 500 NH1 ARG A 472 O HOH A 702 2.18 REMARK 500 O HOH B 708 O HOH B 755 2.18 REMARK 500 OD1 ASP A 306 O HOH A 703 2.18 REMARK 500 O HOH B 705 O HOH B 890 2.19 REMARK 500 OE2 GLU A 504 NH2 ARG A 508 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 LYS A 251 12.74 95.40 REMARK 500 THR A 252 -75.59 -144.51 REMARK 500 GLU A 253 173.45 134.42 REMARK 500 GLN A 254 -88.17 -129.64 REMARK 500 ASP A 256 -121.90 -57.15 REMARK 500 VAL A 257 -15.73 73.13 REMARK 500 ASN A 327 -169.19 -124.57 REMARK 500 ILE A 542 -59.38 -121.42 REMARK 500 ASN B 327 -168.80 -128.25 REMARK 500 ILE B 542 -60.18 -125.04 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 96.8 REMARK 620 3 ASP A 367 OD2 88.3 85.2 REMARK 620 4 ASP A 484 OD1 91.0 89.1 174.1 REMARK 620 5 HOH A 725 O 169.3 93.6 90.0 91.8 REMARK 620 6 HOH A 839 O 88.1 174.1 98.4 87.4 81.7 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 769 O 84.0 REMARK 620 3 HOH A 815 O 87.1 90.1 REMARK 620 4 HOH A 725 O 95.3 93.9 175.5 REMARK 620 5 HOH A 798 O 166.2 84.7 85.1 93.2 REMARK 620 6 HOH A 895 O 98.4 176.4 87.3 88.7 92.6 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 ASN A 417 OD1 REMARK 620 2 HOH A 842 O 95.4 REMARK 620 3 HOH A 867 O 86.1 142.2 REMARK 620 4 HOH A 918 O 92.0 129.1 88.4 REMARK 620 5 HOH A 717 O 87.5 60.9 156.6 69.3 REMARK 620 6 HOH A 836 O 172.6 89.3 86.6 89.4 99.8 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 ASP A 467 OD2 REMARK 620 2 ASP A 471 OD2 97.2 REMARK 620 3 HOH A 742 O 176.9 85.9 REMARK 620 4 HOH A 783 O 85.5 89.3 95.1 REMARK 620 5 HOH A 831 O 93.9 89.0 85.7 178.1 REMARK 620 N 1 2 3 4 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 96.6 REMARK 620 3 ASP B 367 OD2 88.6 85.8 REMARK 620 4 ASP B 484 OD1 90.2 88.7 174.2 REMARK 620 5 HOH B 838 O 88.3 173.7 98.2 87.5 REMARK 620 6 HOH B 720 O 169.5 93.9 91.8 90.4 81.2 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 793 O 167.7 REMARK 620 3 HOH B 799 O 87.8 86.9 REMARK 620 4 HOH B 871 O 98.4 92.7 88.7 REMARK 620 5 HOH B 720 O 94.3 91.7 175.6 87.2 REMARK 620 6 HOH B 762 O 83.9 84.9 89.7 177.2 94.3 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 HOH B 754 O REMARK 620 2 HOH B 730 O 82.8 REMARK 620 3 HOH B 891 O 70.5 95.9 REMARK 620 4 HOH A 778 O 112.5 164.4 86.8 REMARK 620 5 HOH A 943 O 107.4 85.5 177.2 92.5 REMARK 620 6 HOH A 932 O 166.8 89.2 100.1 75.2 82.3 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 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 EDO A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DD5 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D5N B 605 DBREF 6FDC A 244 578 UNP Q08499 PDE4D_HUMAN 244 578 DBREF 6FDC B 244 578 UNP Q08499 PDE4D_HUMAN 244 578 SEQADV 6FDC MET A 243 UNP Q08499 INITIATING METHIONINE SEQADV 6FDC ALA A 579 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS A 580 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS A 581 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS A 582 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS A 583 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS A 584 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS A 585 UNP Q08499 EXPRESSION TAG SEQADV 6FDC MET B 243 UNP Q08499 INITIATING METHIONINE SEQADV 6FDC ALA B 579 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS B 580 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS B 581 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS B 582 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS B 583 UNP Q08499 EXPRESSION TAG SEQADV 6FDC HIS B 584 UNP Q08499 EXPRESSION TAG SEQADV 6FDC 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 EDO A 605 10 HET DD5 A 606 60 HET ZN B 601 1 HET MG B 602 1 HET MG B 603 1 HET EDO B 604 10 HET D5N B 605 60 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM DD5 (2~{R})-1-[3-[4-[BIS(FLUORANYL)METHOXY]-3- HETNAM 2 DD5 CYCLOPENTYLOXY-PHENYL]PYRAZOL-1-YL]-3-MORPHOLIN-4-YL- HETNAM 3 DD5 PROPAN-2-OL HETNAM D5N (2~{S})-1-[5-[4-[BIS(FLUORANYL)METHOXY]-3- HETNAM 2 D5N CYCLOPENTYLOXY-PHENYL]PYRAZOL-1-YL]-3-MORPHOLIN-4-YL- HETNAM 3 D5N PROPAN-2-OL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 5(MG 2+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 8 DD5 C22 H29 F2 N3 O4 FORMUL 13 D5N C22 H29 F2 N3 O4 FORMUL 14 HOH *504(H2 O) HELIX 1 AA1 VAL A 257 GLU A 263 1 7 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 LYS A 302 1 7 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 TYR A 389 1 7 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 THR A 575 1 18 HELIX 22 AC4 VAL B 257 LEU B 262 1 6 HELIX 23 AC5 GLU B 263 VAL B 265 5 3 HELIX 24 AC6 HIS B 271 SER B 279 1 9 HELIX 25 AC7 ARG B 282 ARG B 295 1 14 HELIX 26 AC8 ASP B 296 LYS B 302 1 7 HELIX 27 AC9 PRO B 304 HIS B 318 1 15 HELIX 28 AD1 ASN B 327 SER B 343 1 17 HELIX 29 AD2 THR B 344 GLU B 348 5 5 HELIX 30 AD3 THR B 352 HIS B 366 1 15 HELIX 31 AD4 SER B 374 THR B 381 1 8 HELIX 32 AD5 SER B 383 TYR B 389 1 7 HELIX 33 AD6 SER B 393 LEU B 406 1 14 HELIX 34 AD7 LEU B 407 GLU B 409 5 3 HELIX 35 AD8 THR B 419 ALA B 436 1 18 HELIX 36 AD9 THR B 437 SER B 440 5 4 HELIX 37 AE1 LYS B 441 THR B 455 1 15 HELIX 38 AE2 ASN B 468 LEU B 485 1 18 HELIX 39 AE3 SER B 486 LYS B 490 5 5 HELIX 40 AE4 PRO B 491 ARG B 516 1 26 HELIX 41 AE5 SER B 530 ILE B 542 1 13 HELIX 42 AE6 ILE B 542 VAL B 554 1 13 HELIX 43 AE7 ALA B 558 SER B 574 1 17 LINK NE2 HIS A 330 ZN ZN A 601 1555 1555 2.16 LINK NE2 HIS A 366 ZN ZN A 601 1555 1555 2.17 LINK OD1 ASP A 367 MG MG A 602 1555 1555 2.07 LINK OD2 ASP A 367 ZN ZN A 601 1555 1555 2.06 LINK OD1 ASN A 417 MG MG A 604 1555 1555 2.10 LINK OD2 ASP A 467 MG MG A 603 1555 1555 2.03 LINK OD2 ASP A 471 MG MG A 603 1555 1555 2.10 LINK OD1 ASP A 484 ZN ZN A 601 1555 1555 2.11 LINK NE2 HIS B 330 ZN ZN B 601 1555 1555 2.16 LINK NE2 HIS B 366 ZN ZN B 601 1555 1555 2.21 LINK OD1 ASP B 367 MG MG B 602 1555 1555 2.12 LINK OD2 ASP B 367 ZN ZN B 601 1555 1555 2.04 LINK OD1 ASP B 484 ZN ZN B 601 1555 1555 2.14 LINK ZN ZN A 601 O HOH A 725 1555 1555 2.23 LINK ZN ZN A 601 O HOH A 839 1555 1555 2.15 LINK MG MG A 602 O HOH A 769 1555 1555 2.09 LINK MG MG A 602 O HOH A 815 1555 1555 2.15 LINK MG MG A 602 O HOH A 725 1555 1555 2.05 LINK MG MG A 602 O HOH A 798 1555 1555 2.12 LINK MG MG A 602 O HOH A 895 1555 1555 2.06 LINK MG MG A 603 O HOH A 742 1555 1555 2.12 LINK MG MG A 603 O HOH A 783 1555 1555 2.08 LINK MG MG A 604 O HOH A 842 1555 1555 2.33 LINK MG MG A 604 O HOH A 867 1555 1555 2.12 LINK MG MG A 604 O HOH A 918 1555 1555 2.13 LINK ZN ZN B 601 O HOH B 838 1555 1555 2.17 LINK ZN ZN B 601 O HOH B 720 1555 1555 2.18 LINK MG MG B 602 O HOH B 793 1555 1555 2.08 LINK MG MG B 602 O HOH B 799 1555 1555 2.13 LINK MG MG B 602 O HOH B 871 1555 1555 2.04 LINK MG MG B 602 O HOH B 720 1555 1555 2.12 LINK MG MG B 602 O HOH B 762 1555 1555 2.15 LINK MG MG B 603 O HOH B 754 1555 1555 2.12 LINK MG MG B 603 O HOH B 730 1555 1555 2.13 LINK MG MG B 603 O HOH B 891 1555 1555 2.25 LINK MG MG A 603 O HOH A 831 1555 3647 2.10 LINK MG MG A 604 O HOH A 717 1555 4497 2.27 LINK MG MG A 604 O HOH A 836 1555 4497 2.21 LINK MG MG B 603 O HOH A 778 1555 3647 2.13 LINK MG MG B 603 O HOH A 943 1555 3647 2.10 LINK MG MG B 603 O HOH A 932 1555 3647 2.22 CISPEP 1 GLU A 253 GLN A 254 0 1.31 CISPEP 2 HIS A 555 PRO A 556 0 3.40 CISPEP 3 HIS B 555 PRO B 556 0 2.24 SITE 1 AC1 6 HIS A 330 HIS A 366 ASP A 367 ASP A 484 SITE 2 AC1 6 HOH A 725 HOH A 839 SITE 1 AC2 6 ASP A 367 HOH A 725 HOH A 769 HOH A 798 SITE 2 AC2 6 HOH A 815 HOH A 895 SITE 1 AC3 6 ASP A 467 ASP A 471 HIS A 527 HOH A 742 SITE 2 AC3 6 HOH A 783 HOH A 831 SITE 1 AC4 4 ASN A 417 HOH A 842 HOH A 867 HOH A 918 SITE 1 AC5 3 LYS A 428 ASP A 432 HOH A 763 SITE 1 AC6 17 TYR A 325 SER A 374 ASN A 487 PRO A 488 SITE 2 AC6 17 TYR A 495 TRP A 498 THR A 499 ILE A 502 SITE 3 AC6 17 PHE A 506 PRO A 522 MET A 523 CYS A 524 SITE 4 AC6 17 SER A 534 GLN A 535 PHE A 538 HOH A 701 SITE 5 AC6 17 HOH A 768 SITE 1 AC7 6 HIS B 330 HIS B 366 ASP B 367 ASP B 484 SITE 2 AC7 6 HOH B 720 HOH B 838 SITE 1 AC8 6 ASP B 367 HOH B 720 HOH B 762 HOH B 793 SITE 2 AC8 6 HOH B 799 HOH B 871 SITE 1 AC9 6 HOH A 778 HOH A 932 HOH A 943 HOH B 730 SITE 2 AC9 6 HOH B 754 HOH B 891 SITE 1 AD1 5 ASN A 390 HOH A 764 LYS B 428 ILE B 431 SITE 2 AD1 5 ASP B 432 SITE 1 AD2 13 TYR B 325 ASN B 487 PRO B 488 TYR B 495 SITE 2 AD2 13 TRP B 498 THR B 499 PHE B 506 MET B 523 SITE 3 AD2 13 SER B 534 GLN B 535 PHE B 538 ILE B 542 SITE 4 AD2 13 HOH B 705 CRYST1 64.692 98.608 120.165 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 0.015458 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008322 0.00000