HEADER HYDROLASE 13-DEC-17 6F8X TITLE CRYSTAL STRUCTURE OF THE PDE4D CATALYTIC DOMAIN IN COMPLEX WITH GEBR- TITLE 2 26G 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 6F8X 1 LINK REVDAT 2 23-MAY-18 6F8X 1 JRNL REVDAT 1 16-MAY-18 6F8X 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. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 107507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 5400 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 49.2237 - 6.0555 1.00 3416 172 0.1577 0.2126 REMARK 3 2 6.0555 - 4.8077 1.00 3392 182 0.1743 0.1749 REMARK 3 3 4.8077 - 4.2004 1.00 3396 174 0.1486 0.1892 REMARK 3 4 4.2004 - 3.8165 1.00 3396 182 0.1493 0.1701 REMARK 3 5 3.8165 - 3.5430 1.00 3412 183 0.1578 0.1849 REMARK 3 6 3.5430 - 3.3342 1.00 3409 181 0.1645 0.1850 REMARK 3 7 3.3342 - 3.1672 1.00 3395 180 0.1621 0.1977 REMARK 3 8 3.1672 - 3.0294 1.00 3412 182 0.1689 0.2003 REMARK 3 9 3.0294 - 2.9128 1.00 3399 178 0.1773 0.2213 REMARK 3 10 2.9128 - 2.8123 1.00 3361 174 0.1697 0.2410 REMARK 3 11 2.8123 - 2.7243 1.00 3416 184 0.1639 0.2171 REMARK 3 12 2.7243 - 2.6465 1.00 3425 183 0.1681 0.1810 REMARK 3 13 2.6465 - 2.5768 1.00 3377 180 0.1658 0.2078 REMARK 3 14 2.5768 - 2.5139 1.00 3422 181 0.1587 0.2184 REMARK 3 15 2.5139 - 2.4568 1.00 3405 176 0.1650 0.2183 REMARK 3 16 2.4568 - 2.4045 1.00 3379 182 0.1612 0.2259 REMARK 3 17 2.4045 - 2.3564 1.00 3432 182 0.1560 0.1933 REMARK 3 18 2.3564 - 2.3120 1.00 3403 179 0.1552 0.2010 REMARK 3 19 2.3120 - 2.2707 1.00 3421 182 0.1576 0.2201 REMARK 3 20 2.2707 - 2.2322 1.00 3389 174 0.1652 0.2158 REMARK 3 21 2.2322 - 2.1962 1.00 3399 180 0.1683 0.1920 REMARK 3 22 2.1962 - 2.1624 1.00 3430 185 0.1725 0.2184 REMARK 3 23 2.1624 - 2.1306 1.00 3400 182 0.1803 0.2275 REMARK 3 24 2.1306 - 2.1006 1.00 3356 178 0.1738 0.2185 REMARK 3 25 2.1006 - 2.0722 1.00 3427 183 0.1822 0.1995 REMARK 3 26 2.0722 - 2.0453 1.00 3408 180 0.1886 0.2283 REMARK 3 27 2.0453 - 2.0197 1.00 3394 185 0.1992 0.2322 REMARK 3 28 2.0197 - 1.9954 1.00 3389 179 0.2132 0.2626 REMARK 3 29 1.9954 - 1.9722 1.00 3433 180 0.2168 0.2956 REMARK 3 30 1.9722 - 1.9500 1.00 3414 177 0.2388 0.2763 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 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 : 0.007 5472 REMARK 3 ANGLE : 0.932 7442 REMARK 3 CHIRALITY : 0.038 854 REMARK 3 PLANARITY : 0.004 950 REMARK 3 DIHEDRAL : 14.037 2041 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 6F8X 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_1200007796. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-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 : 107507 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 49.208 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 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: 6F6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 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 49.27350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.25100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.91000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.25100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.27350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.91000 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: 2660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 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 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 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 705 O HOH B 786 1.83 REMARK 500 O HOH A 702 O HOH A 835 1.90 REMARK 500 O HOH B 750 O HOH B 795 1.99 REMARK 500 O HOH A 702 O HOH A 860 2.06 REMARK 500 OD2 ASP B 500 O HOH B 701 2.14 REMARK 500 OE2 GLU A 504 NH2 ARG A 508 2.15 REMARK 500 O HOH B 870 O HOH B 904 2.17 REMARK 500 OD1 ASP A 306 O HOH A 701 2.17 REMARK 500 NE2 HIS A 326 O HOH A 702 2.17 REMARK 500 OG1 THR B 575 O HOH B 702 2.17 REMARK 500 O HOH B 705 O HOH B 837 2.17 REMARK 500 OD1 ASP A 511 NH2 ARG A 514 2.18 REMARK 500 O ALA B 579 O HOH B 703 2.18 REMARK 500 OE1 GLU A 261 O HOH A 703 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 322 O HOH B 701 4545 2.16 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 528 44.69 -143.10 REMARK 500 ILE A 542 -59.73 -122.43 REMARK 500 ASN B 327 -169.05 -124.59 REMARK 500 SER B 393 53.12 39.15 REMARK 500 VAL B 458 -165.38 -121.69 REMARK 500 ILE B 542 -63.10 -123.73 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 93.1 REMARK 620 3 ASP A 367 OD2 88.4 85.1 REMARK 620 4 ASP A 484 OD1 89.9 88.9 173.7 REMARK 620 5 HOH A 725 O 170.3 96.6 91.8 91.0 REMARK 620 6 HOH A 835 O 84.9 176.7 97.4 88.5 85.5 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 725 O 96.7 REMARK 620 3 HOH A 801 O 85.5 96.6 REMARK 620 4 HOH A 814 O 87.4 172.1 90.4 REMARK 620 5 HOH A 838 O 168.8 91.3 85.8 85.6 REMARK 620 6 HOH A 860 O 98.3 88.0 173.6 84.7 89.8 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 ASN A 417 OD1 REMARK 620 2 HOH A 704 O 29.4 REMARK 620 3 HOH A 813 O 26.2 3.1 REMARK 620 N 1 2 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 ASP A 467 OD2 REMARK 620 2 ASP A 471 OD2 93.2 REMARK 620 3 HOH A 755 O 91.1 89.9 REMARK 620 4 HOH A 769 O 173.0 92.6 93.0 REMARK 620 5 HOH A 782 O 83.0 89.7 174.1 93.0 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 96.7 REMARK 620 3 ASP B 367 OD2 90.2 84.8 REMARK 620 4 ASP B 484 OD1 86.3 90.3 173.7 REMARK 620 5 HOH B 758 O 165.9 97.3 92.9 91.7 REMARK 620 6 HOH B 786 O 82.6 172.8 102.3 82.5 83.3 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 758 O 98.9 REMARK 620 3 HOH B 765 O 85.1 98.1 REMARK 620 4 HOH B 796 O 168.8 88.9 86.0 REMARK 620 5 HOH B 804 O 89.1 170.6 87.5 83.9 REMARK 620 6 HOH B 837 O 99.7 87.4 172.2 88.5 86.4 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 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 D08 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D08 B 604 DBREF 6F8X A 244 579 UNP Q08499 PDE4D_HUMAN 244 579 DBREF 6F8X B 244 579 UNP Q08499 PDE4D_HUMAN 244 579 SEQADV 6F8X MET A 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F8X ALA A 579 UNP Q08499 SER 579 CONFLICT SEQADV 6F8X HIS A 580 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS A 581 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS A 582 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS A 583 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS A 584 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS A 585 UNP Q08499 EXPRESSION TAG SEQADV 6F8X MET B 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F8X ALA B 579 UNP Q08499 SER 579 CONFLICT SEQADV 6F8X HIS B 580 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS B 581 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS B 582 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS B 583 UNP Q08499 EXPRESSION TAG SEQADV 6F8X HIS B 584 UNP Q08499 EXPRESSION TAG SEQADV 6F8X 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 D08 A 605 59 HET EDO A 606 10 HET EDO A 607 10 HET ZN B 601 1 HET MG B 602 1 HET DMS B 603 10 HET D08 B 604 59 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM D08 2-[(5~{R})-3-(3-CYCLOPENTYLOXY-4-METHOXY-PHENYL)-4,5- HETNAM 2 D08 DIHYDRO-1,2-OXAZOL-5-YL]-~{N},~{N}-BIS(2- HETNAM 3 D08 HYDROXYETHYL)ETHANAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 4(MG 2+) FORMUL 7 D08 2(C21 H30 N2 O6) FORMUL 8 EDO 2(C2 H6 O2) FORMUL 12 DMS C2 H6 O S FORMUL 14 HOH *455(H2 O) HELIX 1 AA1 ASP A 256 LEU A 262 1 7 HELIX 2 AA2 GLU A 263 VAL A 265 5 3 HELIX 3 AA3 HIS A 271 SER A 279 1 9 HELIX 4 AA4 ARG A 282 ARG A 295 1 14 HELIX 5 AA5 ASP A 296 LYS A 302 1 7 HELIX 6 AA6 PRO A 304 HIS A 318 1 15 HELIX 7 AA7 ASN A 327 SER A 343 1 17 HELIX 8 AA8 THR A 344 GLU A 348 5 5 HELIX 9 AA9 THR A 352 HIS A 366 1 15 HELIX 10 AB1 SER A 374 THR A 381 1 8 HELIX 11 AB2 SER A 383 TYR A 389 1 7 HELIX 12 AB3 SER A 393 LEU A 406 1 14 HELIX 13 AB4 LEU A 407 GLU A 409 5 3 HELIX 14 AB5 THR A 419 ALA A 436 1 18 HELIX 15 AB6 THR A 437 SER A 440 5 4 HELIX 16 AB7 LYS A 441 THR A 455 1 15 HELIX 17 AB8 ASN A 468 LEU A 485 1 18 HELIX 18 AB9 SER A 486 LYS A 490 5 5 HELIX 19 AC1 PRO A 491 ARG A 516 1 26 HELIX 20 AC2 ASP A 525 ALA A 529 5 5 HELIX 21 AC3 SER A 530 ILE A 542 1 13 HELIX 22 AC4 ILE A 542 VAL A 554 1 13 HELIX 23 AC5 ALA A 558 SER A 574 1 17 HELIX 24 AC6 VAL B 257 LEU B 262 1 6 HELIX 25 AC7 GLU B 263 VAL B 265 5 3 HELIX 26 AC8 HIS B 271 SER B 279 1 9 HELIX 27 AC9 ARG B 282 ARG B 295 1 14 HELIX 28 AD1 ASP B 296 PHE B 301 1 6 HELIX 29 AD2 PRO B 304 HIS B 318 1 15 HELIX 30 AD3 ASN B 327 SER B 343 1 17 HELIX 31 AD4 THR B 344 GLU B 348 5 5 HELIX 32 AD5 THR B 352 HIS B 366 1 15 HELIX 33 AD6 SER B 374 THR B 381 1 8 HELIX 34 AD7 SER B 383 TYR B 389 1 7 HELIX 35 AD8 SER B 393 LEU B 406 1 14 HELIX 36 AD9 LEU B 407 GLU B 409 5 3 HELIX 37 AE1 THR B 419 ALA B 436 1 18 HELIX 38 AE2 THR B 437 SER B 440 5 4 HELIX 39 AE3 LYS B 441 THR B 455 1 15 HELIX 40 AE4 ASN B 468 LEU B 485 1 18 HELIX 41 AE5 SER B 486 LYS B 490 5 5 HELIX 42 AE6 PRO B 491 ARG B 516 1 26 HELIX 43 AE7 SER B 530 ILE B 542 1 13 HELIX 44 AE8 ILE B 542 VAL B 554 1 13 HELIX 45 AE9 ALA B 558 SER B 574 1 17 LINK NE2 HIS A 330 ZN ZN A 601 1555 1555 2.17 LINK NE2 HIS A 366 ZN ZN A 601 1555 1555 2.15 LINK OD2 ASP A 367 ZN ZN A 601 1555 1555 2.07 LINK OD1 ASP A 367 MG MG A 602 1555 1555 2.05 LINK OD1 ASN A 417 MG MG A 603 1555 2555 2.08 LINK OD2 ASP A 467 MG MG A 604 1555 1555 2.08 LINK OD2 ASP A 471 MG MG A 604 1555 1555 2.08 LINK OD1 ASP A 484 ZN ZN A 601 1555 1555 2.16 LINK ZN ZN A 601 O HOH A 725 1555 1555 2.12 LINK ZN ZN A 601 O HOH A 835 1555 1555 2.14 LINK MG MG A 602 O HOH A 725 1555 1555 2.16 LINK MG MG A 602 O HOH A 801 1555 1555 2.05 LINK MG MG A 602 O HOH A 814 1555 1555 2.23 LINK MG MG A 602 O HOH A 838 1555 1555 2.18 LINK MG MG A 602 O HOH A 860 1555 1555 2.19 LINK MG MG A 603 O HOH A 704 1555 1555 2.16 LINK MG MG A 603 O HOH A 813 1555 2554 1.99 LINK MG MG A 604 O HOH A 755 1555 4444 2.19 LINK MG MG A 604 O HOH A 769 1555 1555 2.05 LINK MG MG A 604 O HOH A 782 1555 1555 2.10 LINK NE2 HIS B 330 ZN ZN B 601 1555 1555 2.17 LINK NE2 HIS B 366 ZN ZN B 601 1555 1555 2.26 LINK OD2 ASP B 367 ZN ZN B 601 1555 1555 2.09 LINK OD1 ASP B 367 MG MG B 602 1555 1555 2.05 LINK OD1 ASP B 484 ZN ZN B 601 1555 1555 2.13 LINK ZN ZN B 601 O HOH B 758 1555 1555 2.24 LINK ZN ZN B 601 O HOH B 786 1555 1555 2.08 LINK MG MG B 602 O HOH B 758 1555 1555 2.01 LINK MG MG B 602 O HOH B 765 1555 1555 2.08 LINK MG MG B 602 O HOH B 796 1555 1555 2.13 LINK MG MG B 602 O HOH B 804 1555 1555 2.17 LINK MG MG B 602 O HOH B 837 1555 1555 2.15 CISPEP 1 HIS A 555 PRO A 556 0 2.74 CISPEP 2 HIS B 555 PRO B 556 0 3.16 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 835 SITE 1 AC2 6 ASP A 367 HOH A 725 HOH A 801 HOH A 814 SITE 2 AC2 6 HOH A 838 HOH A 860 SITE 1 AC3 3 ASN A 417 HOH A 704 HOH A 813 SITE 1 AC4 6 ASP A 467 ASP A 471 HIS A 527 HOH A 755 SITE 2 AC4 6 HOH A 769 HOH A 782 SITE 1 AC5 21 TYR A 325 HIS A 326 SER A 374 ASN A 375 SITE 2 AC5 21 MET A 439 ASN A 487 ILE A 502 MET A 503 SITE 3 AC5 21 PHE A 506 MET A 523 SER A 534 GLN A 535 SITE 4 AC5 21 PHE A 538 EDO A 606 HOH A 702 HOH A 724 SITE 5 AC5 21 HOH A 735 HOH A 780 HOH A 789 HOH A 791 SITE 6 AC5 21 HOH A 846 SITE 1 AC6 4 GLN A 509 PRO A 522 CYS A 524 D08 A 605 SITE 1 AC7 5 SER A 461 GLY A 462 VAL A 554 HIS A 555 SITE 2 AC7 5 ASP A 557 SITE 1 AC8 7 HIS B 330 HIS B 366 ASP B 367 ASP B 484 SITE 2 AC8 7 MG B 602 HOH B 758 HOH B 786 SITE 1 AC9 7 ASP B 367 ZN B 601 HOH B 758 HOH B 765 SITE 2 AC9 7 HOH B 796 HOH B 804 HOH B 837 SITE 1 AD1 7 ASP A 567 HOH A 799 HOH A 842 ASP B 540 SITE 2 AD1 7 HIS B 544 PRO B 545 GLU B 548 SITE 1 AD2 21 TYR B 325 HIS B 326 SER B 374 ASN B 375 SITE 2 AD2 21 MET B 439 ASN B 487 THR B 499 ILE B 502 SITE 3 AD2 21 MET B 503 MET B 523 SER B 534 GLN B 535 SITE 4 AD2 21 PHE B 538 HOH B 705 HOH B 731 HOH B 745 SITE 5 AD2 21 HOH B 748 HOH B 762 HOH B 789 HOH B 798 SITE 6 AD2 21 HOH B 811 CRYST1 98.547 119.820 64.502 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 0.010147 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015503 0.00000