HEADER HYDROLASE 06-DEC-17 6F6U TITLE CRYSTAL STRUCTURE OF THE PDE4D CATALYTIC DOMAIN IN COMPLEX WITH GEBR- TITLE 2 7B 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; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS PDE4, CATALYTIC DOMAIN, INHIBITOR, GEBR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PROSDOCIMI,S.DONINI,E.PARISINI REVDAT 3 17-JAN-24 6F6U 1 LINK REVDAT 2 23-MAY-18 6F6U 1 JRNL REVDAT 1 16-MAY-18 6F6U 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. 1.83 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 67790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3428 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 45.7227 - 5.2703 1.00 2923 168 0.1581 0.1939 REMARK 3 2 5.2703 - 4.1841 1.00 2809 141 0.1450 0.1810 REMARK 3 3 4.1841 - 3.6555 1.00 2753 157 0.1598 0.1959 REMARK 3 4 3.6555 - 3.3214 1.00 2755 142 0.1779 0.2031 REMARK 3 5 3.3214 - 3.0834 1.00 2714 157 0.1844 0.2412 REMARK 3 6 3.0834 - 2.9016 1.00 2717 164 0.1971 0.2473 REMARK 3 7 2.9016 - 2.7563 1.00 2718 138 0.1942 0.2507 REMARK 3 8 2.7563 - 2.6363 1.00 2717 151 0.1868 0.2243 REMARK 3 9 2.6363 - 2.5349 1.00 2724 139 0.1894 0.2409 REMARK 3 10 2.5349 - 2.4474 1.00 2699 146 0.1965 0.2140 REMARK 3 11 2.4474 - 2.3709 1.00 2686 161 0.1916 0.2546 REMARK 3 12 2.3709 - 2.3031 1.00 2674 143 0.1956 0.2593 REMARK 3 13 2.3031 - 2.2425 1.00 2707 135 0.1954 0.2513 REMARK 3 14 2.2425 - 2.1878 1.00 2709 141 0.1982 0.2561 REMARK 3 15 2.1878 - 2.1380 1.00 2715 142 0.1970 0.2497 REMARK 3 16 2.1380 - 2.0925 1.00 2682 119 0.2003 0.2628 REMARK 3 17 2.0925 - 2.0507 0.99 2681 146 0.2020 0.2682 REMARK 3 18 2.0507 - 2.0120 0.98 2623 138 0.2165 0.3043 REMARK 3 19 2.0120 - 1.9760 0.98 2604 156 0.2176 0.2852 REMARK 3 20 1.9760 - 1.9425 0.97 2593 145 0.2270 0.2781 REMARK 3 21 1.9425 - 1.9112 0.97 2591 133 0.2443 0.3092 REMARK 3 22 1.9112 - 1.8818 0.95 2623 115 0.2525 0.2627 REMARK 3 23 1.8818 - 1.8541 0.95 2536 121 0.2748 0.3073 REMARK 3 24 1.8541 - 1.8280 0.90 2409 130 0.2941 0.3492 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.730 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 5486 REMARK 3 ANGLE : 0.936 7463 REMARK 3 CHIRALITY : 0.036 860 REMARK 3 PLANARITY : 0.005 955 REMARK 3 DIHEDRAL : 13.705 2031 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 6F6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 45.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 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 1.9_1692 REMARK 200 STARTING MODEL: 2PW3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.14 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 32.41350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.76600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.46800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.76600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.41350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.46800 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 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 VAL A 250 CG1 CG2 REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 THR A 252 OG1 CG2 REMARK 470 GLU A 253 CG CD OE1 OE2 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 OD2 ASP A 467 O HOH A 701 2.03 REMARK 500 OD2 ASP A 471 O HOH A 701 2.11 REMARK 500 O GLU B 409 O HOH B 701 2.16 REMARK 500 O HOH B 792 O HOH B 911 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 GLU A 255 85.72 175.18 REMARK 500 ASP A 256 -111.75 -165.43 REMARK 500 VAL A 257 4.80 51.89 REMARK 500 SER A 393 54.03 39.38 REMARK 500 THR A 459 -169.95 -69.31 REMARK 500 ILE A 542 -60.86 -121.87 REMARK 500 ASN B 327 -168.91 -129.13 REMARK 500 THR B 459 -173.99 -68.85 REMARK 500 ILE B 542 -56.70 -127.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1001 DISTANCE = 5.93 ANGSTROMS 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 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 330 NE2 REMARK 620 2 HIS A 366 NE2 96.6 REMARK 620 3 ASP A 367 OD2 88.0 86.9 REMARK 620 4 ASP A 484 OD1 84.8 91.4 172.4 REMARK 620 5 HOH A 783 O 172.0 91.4 91.8 95.6 REMARK 620 6 HOH A 877 O 89.8 173.3 95.3 87.2 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 367 OD1 REMARK 620 2 HOH A 783 O 93.7 REMARK 620 3 HOH A 799 O 83.5 95.6 REMARK 620 4 HOH A 821 O 167.3 92.7 85.1 REMARK 620 5 HOH A 875 O 97.0 91.6 172.8 93.6 REMARK 620 6 HOH A 893 O 90.7 173.8 89.2 83.7 83.6 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 710 O 33.9 REMARK 620 3 HOH A 904 O 29.8 5.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 330 NE2 REMARK 620 2 HIS B 366 NE2 92.7 REMARK 620 3 ASP B 367 OD2 91.4 82.5 REMARK 620 4 ASP B 484 OD1 81.1 91.0 169.8 REMARK 620 5 HOH B 780 O 165.2 101.6 94.3 94.6 REMARK 620 6 HOH B 851 O 87.3 172.6 104.9 81.7 78.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 367 OD1 REMARK 620 2 HOH B 767 O 82.9 REMARK 620 3 HOH B 780 O 101.2 99.4 REMARK 620 4 HOH B 835 O 165.6 86.2 89.8 REMARK 620 5 HOH B 838 O 86.8 91.6 167.1 84.2 REMARK 620 6 HOH B 857 O 102.6 173.4 83.3 87.8 85.1 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 MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN 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 CV8 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CV8 B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 604 DBREF 6F6U A 244 578 UNP Q08499 PDE4D_HUMAN 244 578 DBREF 6F6U B 244 578 UNP Q08499 PDE4D_HUMAN 244 578 SEQADV 6F6U MET A 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F6U ALA A 579 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS A 580 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS A 581 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS A 582 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS A 583 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS A 584 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS A 585 UNP Q08499 EXPRESSION TAG SEQADV 6F6U MET B 243 UNP Q08499 INITIATING METHIONINE SEQADV 6F6U ALA B 579 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS B 580 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS B 581 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS B 582 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS B 583 UNP Q08499 EXPRESSION TAG SEQADV 6F6U HIS B 584 UNP Q08499 EXPRESSION TAG SEQADV 6F6U 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 MG A 601 1 HET ZN A 602 1 HET MG A 603 1 HET CV8 A 604 58 HET GOL A 605 14 HET MG B 601 1 HET ZN B 602 1 HET CV8 B 603 58 HET GOL B 604 14 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM CV8 2-[(~{E})-(3-CYCLOPENTYLOXY-4-METHOXY-PHENYL) HETNAM 2 CV8 METHYLIDENEAMINO]OXY-1-[(2~{R},6~{S})-2,6- HETNAM 3 CV8 DIMETHYLMORPHOLIN-4-YL]ETHANONE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 3(MG 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 6 CV8 2(C21 H30 N2 O5) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 12 HOH *554(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 LYS B 267 5 5 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 PHE B 301 1 6 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 602 1555 1555 2.22 LINK NE2 HIS A 366 ZN ZN A 602 1555 1555 2.16 LINK OD1 ASP A 367 MG MG A 601 1555 1555 2.07 LINK OD2 ASP A 367 ZN ZN A 602 1555 1555 2.15 LINK OD1 ASN A 417 MG MG A 603 1555 4477 2.37 LINK OD1 ASP A 484 ZN ZN A 602 1555 1555 2.17 LINK MG MG A 601 O HOH A 783 1555 1555 2.06 LINK MG MG A 601 O HOH A 799 1555 1555 2.15 LINK MG MG A 601 O HOH A 821 1555 1555 2.15 LINK MG MG A 601 O HOH A 875 1555 1555 2.19 LINK MG MG A 601 O HOH A 893 1555 1555 2.08 LINK ZN ZN A 602 O HOH A 783 1555 1555 2.11 LINK ZN ZN A 602 O HOH A 877 1555 1555 2.26 LINK MG MG A 603 O HOH A 710 1555 1555 2.68 LINK MG MG A 603 O HOH A 904 1555 4577 1.96 LINK NE2 HIS B 330 ZN ZN B 602 1555 1555 2.21 LINK NE2 HIS B 366 ZN ZN B 602 1555 1555 2.21 LINK OD1 ASP B 367 MG MG B 601 1555 1555 2.06 LINK OD2 ASP B 367 ZN ZN B 602 1555 1555 2.12 LINK OD1 ASP B 484 ZN ZN B 602 1555 1555 2.22 LINK MG MG B 601 O HOH B 767 1555 1555 2.19 LINK MG MG B 601 O HOH B 780 1555 1555 1.99 LINK MG MG B 601 O HOH B 835 1555 1555 2.00 LINK MG MG B 601 O HOH B 838 1555 1555 2.19 LINK MG MG B 601 O HOH B 857 1555 1555 2.03 LINK ZN ZN B 602 O HOH B 780 1555 1555 2.12 LINK ZN ZN B 602 O HOH B 851 1555 1555 2.18 CISPEP 1 GLU A 255 ASP A 256 0 -6.23 CISPEP 2 HIS A 555 PRO A 556 0 3.95 CISPEP 3 HIS B 555 PRO B 556 0 3.00 SITE 1 AC1 7 ASP A 367 ZN A 602 HOH A 783 HOH A 799 SITE 2 AC1 7 HOH A 821 HOH A 875 HOH A 893 SITE 1 AC2 7 HIS A 330 HIS A 366 ASP A 367 ASP A 484 SITE 2 AC2 7 MG A 601 HOH A 783 HOH A 877 SITE 1 AC3 4 ASP A 264 ASN A 417 HOH A 710 HOH A 904 SITE 1 AC4 13 TYR A 325 SER A 374 MET A 439 ASN A 487 SITE 2 AC4 13 THR A 499 ILE A 502 PHE A 506 GLN A 509 SITE 3 AC4 13 MET A 523 CYS A 524 GLN A 535 PHE A 538 SITE 4 AC4 13 HOH A 786 SITE 1 AC5 8 HIS A 398 VAL A 402 HOH A 716 HOH A 755 SITE 2 AC5 8 HOH A 824 MET B 388 TRP B 571 SER B 574 SITE 1 AC6 7 ASP B 367 ZN B 602 HOH B 767 HOH B 780 SITE 2 AC6 7 HOH B 835 HOH B 838 HOH B 857 SITE 1 AC7 7 HIS B 330 HIS B 366 ASP B 367 ASP B 484 SITE 2 AC7 7 MG B 601 HOH B 780 HOH B 851 SITE 1 AC8 14 TYR B 325 MET B 439 ASN B 487 TRP B 498 SITE 2 AC8 14 THR B 499 ILE B 502 MET B 503 PHE B 506 SITE 3 AC8 14 GLN B 535 PHE B 538 HOH B 706 HOH B 709 SITE 4 AC8 14 HOH B 735 HOH B 823 SITE 1 AC9 1 HOH B 717 CRYST1 64.827 98.936 119.532 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 0.015426 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008366 0.00000