HEADER HYDROLASE 14-DEC-20 7B9H TITLE CRYSTAL STRUCTURE OF THE PDE4D CATALYTIC DOMAIN IN COMPLEX WITH GEBR- TITLE 2 42A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPDE3,PDE43; COMPND 5 EC: 3.1.4.53; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDE4D, DPDE3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHODIESTERASE 4D, INHIBITOR, COMPLEX, GEBR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.TORRETTA,S.ABBATE,E.PARISINI REVDAT 3 31-JAN-24 7B9H 1 REMARK REVDAT 2 07-JUL-21 7B9H 1 JRNL REVDAT 1 30-JUN-21 7B9H 0 JRNL AUTH C.BRULLO,F.RAPETTI,S.ABBATE,T.PROSDOCIMI,A.TORRETTA, JRNL AUTH 2 M.SEMRAU,M.MASSA,S.ALFEI,P.STORICI,E.PARISINI,O.BRUNO JRNL TITL DESIGN, SYNTHESIS, BIOLOGICAL EVALUATION AND STRUCTURAL JRNL TITL 2 CHARACTERIZATION OF NOVEL GEBR LIBRARY PDE4D INHIBITORS. JRNL REF EUR.J.MED.CHEM. V. 223 13638 2021 JRNL REFN ISSN 0223-5234 JRNL PMID 34171658 JRNL DOI 10.1016/J.EJMECH.2021.113638 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19RC7_4070 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 122638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 6199 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 54.1300 - 4.6600 1.00 4173 227 0.1643 0.1755 REMARK 3 2 4.6600 - 3.7000 1.00 4054 180 0.1478 0.1639 REMARK 3 3 3.7000 - 3.2300 1.00 3959 218 0.1666 0.1989 REMARK 3 4 3.2300 - 2.9400 1.00 3967 192 0.1746 0.2302 REMARK 3 5 2.9400 - 2.7300 1.00 3909 236 0.1799 0.1894 REMARK 3 6 2.7300 - 2.5600 1.00 3933 196 0.1765 0.1982 REMARK 3 7 2.5600 - 2.4400 1.00 3913 232 0.1786 0.1791 REMARK 3 8 2.4400 - 2.3300 1.00 3908 203 0.1789 0.2175 REMARK 3 9 2.3300 - 2.2400 0.99 3829 213 0.2151 0.2695 REMARK 3 10 2.2400 - 2.1600 0.99 3898 181 0.1971 0.2251 REMARK 3 11 2.1600 - 2.1000 1.00 3888 200 0.1947 0.1975 REMARK 3 12 2.1000 - 2.0400 1.00 3861 203 0.2318 0.2719 REMARK 3 13 2.0400 - 1.9800 1.00 3902 201 0.2003 0.2389 REMARK 3 14 1.9800 - 1.9300 1.00 3878 189 0.2195 0.2589 REMARK 3 15 1.9300 - 1.8900 0.97 3791 189 0.3477 0.3854 REMARK 3 16 1.8900 - 1.8500 1.00 3866 205 0.2289 0.2508 REMARK 3 17 1.8500 - 1.8100 1.00 3887 207 0.2110 0.2298 REMARK 3 18 1.8100 - 1.7800 1.00 3904 206 0.2176 0.2671 REMARK 3 19 1.7800 - 1.7500 1.00 3854 186 0.2314 0.2528 REMARK 3 20 1.7500 - 1.7200 1.00 3869 219 0.2444 0.2592 REMARK 3 21 1.7200 - 1.6900 1.00 3878 194 0.2314 0.2735 REMARK 3 22 1.6900 - 1.6600 1.00 3816 213 0.2148 0.2667 REMARK 3 23 1.6600 - 1.6400 1.00 3868 224 0.2291 0.2592 REMARK 3 24 1.6400 - 1.6200 1.00 3818 216 0.2223 0.2481 REMARK 3 25 1.6200 - 1.5900 1.00 3887 220 0.2339 0.2746 REMARK 3 26 1.5900 - 1.5700 1.00 3829 199 0.2430 0.2579 REMARK 3 27 1.5700 - 1.5500 0.99 3823 218 0.2658 0.3003 REMARK 3 28 1.5500 - 1.5300 0.99 3828 174 0.2884 0.2912 REMARK 3 29 1.5300 - 1.5200 0.98 3761 204 0.4352 0.4365 REMARK 3 30 1.5200 - 1.5000 0.97 3688 254 0.3619 0.3847 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.93 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7B9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-18 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : M 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 122986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 54.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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: 2PW3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM CHLORIDE, HEPES, 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 32.37400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.91050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.31400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.91050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.37400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.31400 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: 7520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 77 REMARK 465 SER A 78 REMARK 465 ILE A 79 REMARK 465 GLN A 412 REMARK 465 ALA A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 HIS A 417 REMARK 465 HIS A 418 REMARK 465 HIS A 419 REMARK 465 MET B 77 REMARK 465 SER B 78 REMARK 465 ILE B 79 REMARK 465 PRO B 80 REMARK 465 ARG B 81 REMARK 465 PHE B 82 REMARK 465 GLY B 83 REMARK 465 VAL B 84 REMARK 465 LYS B 85 REMARK 465 THR B 86 REMARK 465 GLU B 87 REMARK 465 HIS B 415 REMARK 465 HIS B 416 REMARK 465 HIS B 417 REMARK 465 HIS B 418 REMARK 465 HIS B 419 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 694 O HOH A 965 2.18 REMARK 500 O HOH B 827 O HOH B 857 2.18 REMARK 500 O HOH A 861 O HOH A 964 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 OE1 GLU B 288 O2 EDO A 517 3645 2.09 REMARK 500 OE2 GLU A 218 NZ LYS B 367 3555 2.10 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 LEU A 104 142.13 -35.97 REMARK 500 ASN A 161 -169.70 -125.55 REMARK 500 THR A 293 -171.37 -67.37 REMARK 500 ILE A 376 -60.06 -123.17 REMARK 500 ASN B 161 -166.65 -128.39 REMARK 500 ALA B 183 18.86 57.65 REMARK 500 SER B 227 56.68 37.28 REMARK 500 THR B 293 -170.28 -64.16 REMARK 500 SER B 294 -82.82 -57.54 REMARK 500 SER B 295 -12.06 -26.48 REMARK 500 MET B 357 10.41 83.46 REMARK 500 ILE B 376 -61.30 -127.80 REMARK 500 ILE B 376 -60.99 -128.03 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 164 NE2 REMARK 620 2 HIS A 200 NE2 95.5 REMARK 620 3 ASP A 201 OD2 89.0 84.8 REMARK 620 4 ASP A 318 OD1 88.2 89.9 173.7 REMARK 620 5 HOH A 632 O 169.1 95.3 91.0 92.8 REMARK 620 6 HOH A 781 O 86.8 174.8 99.9 85.5 82.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 201 OD1 REMARK 620 2 HOH A 632 O 91.7 REMARK 620 3 HOH A 707 O 166.3 96.5 REMARK 620 4 HOH A 713 O 84.8 95.9 83.4 REMARK 620 5 HOH A 720 O 87.7 172.9 85.6 91.1 REMARK 620 6 HOH A 854 O 98.6 88.5 92.7 174.5 84.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 251 OD1 REMARK 620 2 HOH A 619 O 169.9 REMARK 620 3 HOH A 817 O 88.9 87.7 REMARK 620 4 HOH A 827 O 92.6 97.3 98.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 301 OD2 REMARK 620 2 ASP A 305 OD2 100.9 REMARK 620 3 HOH A 608 O 173.9 85.1 REMARK 620 4 HOH A 701 O 86.3 86.9 95.1 REMARK 620 5 HOH A 802 O 95.1 87.5 84.1 174.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 687 O REMARK 620 2 HOH A 711 O 84.4 REMARK 620 3 HOH A 956 O 98.1 96.6 REMARK 620 4 HOH B 648 O 93.9 176.7 86.4 REMARK 620 5 HOH B 677 O 97.4 89.8 163.7 87.6 REMARK 620 6 HOH B 910 O 170.0 88.4 75.9 93.7 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 633 O REMARK 620 2 HOH A 685 O 87.5 REMARK 620 3 HOH A 874 O 78.3 95.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 653 O REMARK 620 2 HOH A 670 O 76.1 REMARK 620 3 HOH A 886 O 67.4 89.2 REMARK 620 4 HOH B 605 O 87.0 162.4 79.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 705 O REMARK 620 2 HOH B 638 O 98.2 REMARK 620 3 HOH B 686 O 171.5 89.0 REMARK 620 4 HOH B 762 O 89.3 171.1 83.9 REMARK 620 5 HOH B 773 O 87.0 96.2 87.7 89.0 REMARK 620 6 HOH B 850 O 88.3 81.8 97.2 93.7 174.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 95.2 REMARK 620 3 ASP B 201 OD2 86.5 85.4 REMARK 620 4 ASP B 318 OD1 89.3 90.2 173.7 REMARK 620 5 HOH B 642 O 168.1 96.6 93.1 92.0 REMARK 620 6 HOH B 726 O 87.8 176.5 96.7 87.9 80.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 642 O 92.7 REMARK 620 3 HOH B 684 O 83.2 96.1 REMARK 620 4 HOH B 708 O 166.9 92.7 84.4 REMARK 620 5 HOH B 730 O 88.9 172.9 90.9 87.2 REMARK 620 6 HOH B 801 O 100.0 87.1 175.4 92.2 85.8 REMARK 620 N 1 2 3 4 5 DBREF 7B9H A 78 412 UNP Q08499 PDE4D_HUMAN 244 578 DBREF 7B9H B 78 412 UNP Q08499 PDE4D_HUMAN 244 578 SEQADV 7B9H MET A 77 UNP Q08499 INITIATING METHIONINE SEQADV 7B9H ALA A 413 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS A 414 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS A 415 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS A 416 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS A 417 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS A 418 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS A 419 UNP Q08499 EXPRESSION TAG SEQADV 7B9H MET B 77 UNP Q08499 INITIATING METHIONINE SEQADV 7B9H ALA B 413 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS B 414 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS B 415 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS B 416 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS B 417 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS B 418 UNP Q08499 EXPRESSION TAG SEQADV 7B9H HIS B 419 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 501 1 HET MG A 502 1 HET MG A 503 1 HET MG A 504 1 HET MG A 505 1 HET MG A 506 1 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HET EDO A 512 4 HET EDO A 513 4 HET EDO A 514 4 HET EDO A 515 8 HET EDO A 516 4 HET EDO A 517 4 HET EDO A 518 4 HET EDO A 519 4 HET EDO A 520 4 HET EDO A 521 4 HET EDO A 522 4 HET EDO A 523 4 HET T3K A 524 28 HET ZN B 501 1 HET MG B 502 1 HET MG B 503 1 HET MG B 504 1 HET EDO B 505 4 HET EDO B 506 4 HET EDO B 507 4 HET EDO B 508 4 HET EDO B 509 4 HET EDO B 510 4 HET EDO B 511 4 HET EDO B 512 4 HET EDO B 513 4 HET EDO B 514 4 HET EDO B 515 4 HET T3K B 516 28 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM T3K 3-[(~{E})-1-(3-CYCLOPENTYLOXY-4-METHOXY-PHENYL) HETNAM 2 T3K ETHYLIDENEAMINO]OXY-1-MORPHOLIN-4-YL-PROPAN-1-ONE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 8(MG 2+) FORMUL 9 EDO 28(C2 H6 O2) FORMUL 26 T3K 2(C21 H30 N2 O5) FORMUL 43 HOH *686(H2 O) HELIX 1 AA1 GLN A 88 GLU A 97 1 10 HELIX 2 AA2 HIS A 105 SER A 113 1 9 HELIX 3 AA3 ARG A 116 ARG A 129 1 14 HELIX 4 AA4 ASP A 130 LYS A 136 1 7 HELIX 5 AA5 PRO A 138 HIS A 152 1 15 HELIX 6 AA6 ASN A 161 SER A 177 1 17 HELIX 7 AA7 THR A 178 GLU A 182 5 5 HELIX 8 AA8 THR A 186 HIS A 200 1 15 HELIX 9 AA9 SER A 208 THR A 215 1 8 HELIX 10 AB1 SER A 217 ASN A 224 1 8 HELIX 11 AB2 SER A 227 LEU A 240 1 14 HELIX 12 AB3 LEU A 241 GLU A 243 5 3 HELIX 13 AB4 THR A 253 ALA A 270 1 18 HELIX 14 AB5 THR A 271 SER A 274 5 4 HELIX 15 AB6 LYS A 275 THR A 289 1 15 HELIX 16 AB7 ASN A 302 LEU A 319 1 18 HELIX 17 AB8 SER A 320 LYS A 324 5 5 HELIX 18 AB9 PRO A 325 ARG A 350 1 26 HELIX 19 AC1 SER A 364 ILE A 376 1 13 HELIX 20 AC2 ILE A 376 VAL A 388 1 13 HELIX 21 AC3 ALA A 392 THR A 409 1 18 HELIX 22 AC4 GLU B 89 LEU B 96 1 8 HELIX 23 AC5 GLU B 97 VAL B 99 5 3 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ARG B 129 1 14 HELIX 26 AC8 ASP B 130 PHE B 135 1 6 HELIX 27 AC9 PRO B 138 HIS B 152 1 15 HELIX 28 AD1 ASN B 161 SER B 177 1 17 HELIX 29 AD2 THR B 178 GLU B 182 5 5 HELIX 30 AD3 THR B 186 HIS B 200 1 15 HELIX 31 AD4 SER B 208 THR B 215 1 8 HELIX 32 AD5 SER B 217 ASN B 224 1 8 HELIX 33 AD6 SER B 227 LEU B 240 1 14 HELIX 34 AD7 LEU B 241 GLU B 243 5 3 HELIX 35 AD8 THR B 253 ALA B 270 1 18 HELIX 36 AD9 THR B 271 SER B 274 5 4 HELIX 37 AE1 LYS B 275 THR B 289 1 15 HELIX 38 AE2 ASN B 302 LEU B 319 1 18 HELIX 39 AE3 SER B 320 LYS B 324 5 5 HELIX 40 AE4 PRO B 325 ARG B 350 1 26 HELIX 41 AE5 SER B 364 ILE B 376 1 13 HELIX 42 AE6 ILE B 376 VAL B 388 1 13 HELIX 43 AE7 ALA B 392 SER B 408 1 17 LINK CG AMET A 273 C19 T3K A 524 1555 1555 1.50 LINK NE2 HIS A 164 ZN ZN A 501 1555 1555 2.15 LINK NE2 HIS A 200 ZN ZN A 501 1555 1555 2.21 LINK OD2 ASP A 201 ZN ZN A 501 1555 1555 2.03 LINK OD1 ASP A 201 MG MG A 502 1555 1555 2.07 LINK OD1 ASN A 251 MG MG A 504 1555 1555 2.10 LINK OD2 ASP A 301 MG MG A 505 1555 1555 2.07 LINK OD2 ASP A 305 MG MG A 505 1555 1555 2.05 LINK OD1 ASP A 318 ZN ZN A 501 1555 1555 2.16 LINK ZN ZN A 501 O HOH A 632 1555 1555 2.01 LINK ZN ZN A 501 O HOH A 781 1555 1555 2.19 LINK MG MG A 502 O HOH A 632 1555 1555 2.14 LINK MG MG A 502 O HOH A 707 1555 1555 2.12 LINK MG MG A 502 O HOH A 713 1555 1555 2.06 LINK MG MG A 502 O HOH A 720 1555 1555 2.22 LINK MG MG A 502 O HOH A 854 1555 1555 2.09 LINK MG MG A 503 O HOH A 687 1555 1555 2.00 LINK MG MG A 503 O HOH A 711 1555 1555 2.06 LINK MG MG A 503 O HOH A 956 1555 1555 2.12 LINK MG MG A 503 O HOH B 648 1555 2554 2.16 LINK MG MG A 503 O HOH B 677 1555 2554 2.03 LINK MG MG A 503 O HOH B 910 1555 2554 2.24 LINK MG MG A 504 O HOH A 619 1555 4455 2.17 LINK MG MG A 504 O HOH A 817 1555 1555 2.07 LINK MG MG A 504 O HOH A 827 1555 1555 1.99 LINK MG MG A 505 O HOH A 608 1555 1555 2.12 LINK MG MG A 505 O HOH A 701 1555 1555 2.01 LINK MG MG A 505 O HOH A 802 1555 1555 2.11 LINK MG MG A 506 O HOH A 633 1555 1555 2.01 LINK MG MG A 506 O HOH A 685 1555 3655 2.10 LINK MG MG A 506 O HOH A 874 1555 3655 2.13 LINK O HOH A 653 MG MG B 503 3545 1555 2.23 LINK O HOH A 670 MG MG B 503 3545 1555 2.29 LINK O HOH A 705 MG MG B 504 3645 1555 2.09 LINK O HOH A 886 MG MG B 503 3545 1555 2.45 LINK NE2 HIS B 164 ZN ZN B 501 1555 1555 2.19 LINK NE2 HIS B 200 ZN ZN B 501 1555 1555 2.20 LINK OD2 ASP B 201 ZN ZN B 501 1555 1555 2.09 LINK OD1 ASP B 201 MG MG B 502 1555 1555 2.09 LINK OD1 ASP B 318 ZN ZN B 501 1555 1555 2.13 LINK ZN ZN B 501 O HOH B 642 1555 1555 2.11 LINK ZN ZN B 501 O HOH B 726 1555 1555 2.28 LINK MG MG B 502 O HOH B 642 1555 1555 2.12 LINK MG MG B 502 O HOH B 684 1555 1555 2.14 LINK MG MG B 502 O HOH B 708 1555 1555 2.08 LINK MG MG B 502 O HOH B 730 1555 1555 2.17 LINK MG MG B 502 O HOH B 801 1555 1555 2.10 LINK MG MG B 503 O HOH B 605 1555 1555 2.09 LINK MG MG B 504 O HOH B 638 1555 1555 2.27 LINK MG MG B 504 O HOH B 686 1555 1555 2.06 LINK MG MG B 504 O HOH B 762 1555 1555 2.43 LINK MG MG B 504 O HOH B 773 1555 1555 2.08 LINK MG MG B 504 O HOH B 850 1555 1555 2.17 CISPEP 1 HIS A 389 PRO A 390 0 0.04 CISPEP 2 HIS B 389 PRO B 390 0 6.50 CRYST1 64.748 98.628 119.821 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 0.015444 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010139 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008346 0.00000