HEADER HYDROLASE 23-JUL-19 6KJZ TITLE CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN COMPLEXED WITH COMPOUND 1 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PDE4 INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.HUANG,X.HE,H.-B.LUO REVDAT 4 22-NOV-23 6KJZ 1 LINK REVDAT 3 13-MAY-20 6KJZ 1 TITLE REVDAT 2 08-APR-20 6KJZ 1 JRNL REVDAT 1 18-MAR-20 6KJZ 0 JRNL AUTH J.LIANG,Y.Y.HUANG,Q.ZHOU,Y.GAO,Z.LI,D.WU,S.YU,L.GUO,Z.CHEN, JRNL AUTH 2 L.HUANG,S.H.LIANG,X.HE,R.WU,H.B.LUO JRNL TITL DISCOVERY AND OPTIMIZATION OF ALPHA-MANGOSTIN DERIVATIVES AS JRNL TITL 2 NOVEL PDE4 INHIBITORS FOR THE TREATMENT OF VASCULAR JRNL TITL 3 DEMENTIA. JRNL REF J.MED.CHEM. V. 63 3370 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32115956 JRNL DOI 10.1021/ACS.JMEDCHEM.0C00060 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.371 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 39757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.804 REMARK 3 FREE R VALUE TEST SET COUNT : 1910 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 22.1400 - 5.2800 0.95 2771 145 0.1600 0.1876 REMARK 3 2 5.2800 - 4.2002 0.99 2741 149 0.1574 0.2105 REMARK 3 3 4.2002 - 3.6720 0.99 2723 143 0.1811 0.2246 REMARK 3 4 3.6720 - 3.3375 1.00 2751 130 0.1981 0.2558 REMARK 3 5 3.3375 - 3.0990 1.00 2715 123 0.2182 0.2538 REMARK 3 6 3.0990 - 2.9167 1.00 2718 152 0.2221 0.2539 REMARK 3 7 2.9167 - 2.7709 1.00 2712 125 0.2280 0.2760 REMARK 3 8 2.7709 - 2.6505 1.00 2675 156 0.2304 0.2994 REMARK 3 9 2.6505 - 2.5486 1.00 2669 148 0.2292 0.3091 REMARK 3 10 2.5486 - 2.4608 1.00 2724 116 0.2347 0.2455 REMARK 3 11 2.4608 - 2.3839 1.00 2669 141 0.2228 0.2417 REMARK 3 12 2.3839 - 2.3159 1.00 2713 126 0.2351 0.2972 REMARK 3 13 2.3159 - 2.2550 0.99 2639 137 0.2555 0.3115 REMARK 3 14 2.2550 - 2.2100 0.98 2627 119 0.2200 0.3198 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) : 0.264 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.886 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.21 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 : 0.008 5477 REMARK 3 ANGLE : 0.871 7452 REMARK 3 CHIRALITY : 0.045 849 REMARK 3 PLANARITY : 0.006 1012 REMARK 3 DIHEDRAL : 15.393 3292 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 6KJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION NOVA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 38.41 REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 38.41 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40198 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 22.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.160 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.10 REMARK 200 STARTING MODEL: 5WQA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.4), 0.1 M MGCL2, 15 REMARK 280 -20% PE G3350, 10% ISOPROPANOL, 25% ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 277K 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 29.65550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.65800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.65800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.65550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.85000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLN A 412 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 GLU B 382 O HOH B 601 2.02 REMARK 500 OG SER B 226 O HOH B 602 2.10 REMARK 500 O HOH A 666 O HOH A 709 2.13 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 OE2 GLU A 244 OG1 THR B 253 3454 2.09 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 MET A 357 -7.75 77.44 REMARK 500 ILE A 376 -64.41 -133.95 REMARK 500 THR B 253 173.42 -59.65 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 B 711 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B 712 DISTANCE = 6.45 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 164 NE2 REMARK 620 2 HIS A 200 NE2 91.8 REMARK 620 3 ASP A 201 OD2 86.3 84.9 REMARK 620 4 ASP A 318 OD1 86.2 94.3 172.5 REMARK 620 5 HOH A 635 O 173.1 92.6 88.8 98.7 REMARK 620 6 HOH A 693 O 86.8 178.5 95.6 85.1 88.8 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 635 O 96.0 REMARK 620 3 HOH A 636 O 157.2 91.0 REMARK 620 4 HOH A 648 O 77.2 88.1 81.3 REMARK 620 5 HOH A 659 O 84.8 172.9 85.7 85.2 REMARK 620 6 HOH A 689 O 107.1 94.0 94.0 174.9 92.5 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 83.9 REMARK 620 3 ASP B 201 OD2 84.9 77.0 REMARK 620 4 ASP B 318 OD2 87.6 87.9 163.8 REMARK 620 5 HOH B 634 O 94.6 177.6 104.8 90.1 REMARK 620 6 HOH B 639 O 178.7 97.3 95.1 92.8 84.1 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 612 O 80.8 REMARK 620 3 HOH B 614 O 161.1 89.1 REMARK 620 4 HOH B 639 O 103.1 101.9 94.6 REMARK 620 5 HOH B 652 O 84.4 86.6 79.1 169.4 REMARK 620 6 HOH B 670 O 99.6 170.0 87.6 87.8 83.5 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MKU A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MKU B 503 DBREF 6KJZ A 85 412 UNP Q08499 PDE4D_HUMAN 387 714 DBREF 6KJZ B 85 412 UNP Q08499 PDE4D_HUMAN 387 714 SEQRES 1 A 328 LYS THR GLU GLN GLU ASP VAL LEU ALA LYS GLU LEU GLU SEQRES 2 A 328 ASP VAL ASN LYS TRP GLY LEU HIS VAL PHE ARG ILE ALA SEQRES 3 A 328 GLU LEU SER GLY ASN ARG PRO LEU THR VAL ILE MET HIS SEQRES 4 A 328 THR ILE PHE GLN GLU ARG ASP LEU LEU LYS THR PHE LYS SEQRES 5 A 328 ILE PRO VAL ASP THR LEU ILE THR TYR LEU MET THR LEU SEQRES 6 A 328 GLU ASP HIS TYR HIS ALA ASP VAL ALA TYR HIS ASN ASN SEQRES 7 A 328 ILE HIS ALA ALA ASP VAL VAL GLN SER THR HIS VAL LEU SEQRES 8 A 328 LEU SER THR PRO ALA LEU GLU ALA VAL PHE THR ASP LEU SEQRES 9 A 328 GLU ILE LEU ALA ALA ILE PHE ALA SER ALA ILE HIS ASP SEQRES 10 A 328 VAL ASP HIS PRO GLY VAL SER ASN GLN PHE LEU ILE ASN SEQRES 11 A 328 THR ASN SER GLU LEU ALA LEU MET TYR ASN ASP SER SER SEQRES 12 A 328 VAL LEU GLU ASN HIS HIS LEU ALA VAL GLY PHE LYS LEU SEQRES 13 A 328 LEU GLN GLU GLU ASN CYS ASP ILE PHE GLN ASN LEU THR SEQRES 14 A 328 LYS LYS GLN ARG GLN SER LEU ARG LYS MET VAL ILE ASP SEQRES 15 A 328 ILE VAL LEU ALA THR ASP MET SER LYS HIS MET ASN LEU SEQRES 16 A 328 LEU ALA ASP LEU LYS THR MET VAL GLU THR LYS LYS VAL SEQRES 17 A 328 THR SER SER GLY VAL LEU LEU LEU ASP ASN TYR SER ASP SEQRES 18 A 328 ARG ILE GLN VAL LEU GLN ASN MET VAL HIS CYS ALA ASP SEQRES 19 A 328 LEU SER ASN PRO THR LYS PRO LEU GLN LEU TYR ARG GLN SEQRES 20 A 328 TRP THR ASP ARG ILE MET GLU GLU PHE PHE ARG GLN GLY SEQRES 21 A 328 ASP ARG GLU ARG GLU ARG GLY MET GLU ILE SER PRO MET SEQRES 22 A 328 CYS ASP LYS HIS ASN ALA SER VAL GLU LYS SER GLN VAL SEQRES 23 A 328 GLY PHE ILE ASP TYR ILE VAL HIS PRO LEU TRP GLU THR SEQRES 24 A 328 TRP ALA ASP LEU VAL HIS PRO ASP ALA GLN ASP ILE LEU SEQRES 25 A 328 ASP THR LEU GLU ASP ASN ARG GLU TRP TYR GLN SER THR SEQRES 26 A 328 ILE PRO GLN SEQRES 1 B 328 LYS THR GLU GLN GLU ASP VAL LEU ALA LYS GLU LEU GLU SEQRES 2 B 328 ASP VAL ASN LYS TRP GLY LEU HIS VAL PHE ARG ILE ALA SEQRES 3 B 328 GLU LEU SER GLY ASN ARG PRO LEU THR VAL ILE MET HIS SEQRES 4 B 328 THR ILE PHE GLN GLU ARG ASP LEU LEU LYS THR PHE LYS SEQRES 5 B 328 ILE PRO VAL ASP THR LEU ILE THR TYR LEU MET THR LEU SEQRES 6 B 328 GLU ASP HIS TYR HIS ALA ASP VAL ALA TYR HIS ASN ASN SEQRES 7 B 328 ILE HIS ALA ALA ASP VAL VAL GLN SER THR HIS VAL LEU SEQRES 8 B 328 LEU SER THR PRO ALA LEU GLU ALA VAL PHE THR ASP LEU SEQRES 9 B 328 GLU ILE LEU ALA ALA ILE PHE ALA SER ALA ILE HIS ASP SEQRES 10 B 328 VAL ASP HIS PRO GLY VAL SER ASN GLN PHE LEU ILE ASN SEQRES 11 B 328 THR ASN SER GLU LEU ALA LEU MET TYR ASN ASP SER SER SEQRES 12 B 328 VAL LEU GLU ASN HIS HIS LEU ALA VAL GLY PHE LYS LEU SEQRES 13 B 328 LEU GLN GLU GLU ASN CYS ASP ILE PHE GLN ASN LEU THR SEQRES 14 B 328 LYS LYS GLN ARG GLN SER LEU ARG LYS MET VAL ILE ASP SEQRES 15 B 328 ILE VAL LEU ALA THR ASP MET SER LYS HIS MET ASN LEU SEQRES 16 B 328 LEU ALA ASP LEU LYS THR MET VAL GLU THR LYS LYS VAL SEQRES 17 B 328 THR SER SER GLY VAL LEU LEU LEU ASP ASN TYR SER ASP SEQRES 18 B 328 ARG ILE GLN VAL LEU GLN ASN MET VAL HIS CYS ALA ASP SEQRES 19 B 328 LEU SER ASN PRO THR LYS PRO LEU GLN LEU TYR ARG GLN SEQRES 20 B 328 TRP THR ASP ARG ILE MET GLU GLU PHE PHE ARG GLN GLY SEQRES 21 B 328 ASP ARG GLU ARG GLU ARG GLY MET GLU ILE SER PRO MET SEQRES 22 B 328 CYS ASP LYS HIS ASN ALA SER VAL GLU LYS SER GLN VAL SEQRES 23 B 328 GLY PHE ILE ASP TYR ILE VAL HIS PRO LEU TRP GLU THR SEQRES 24 B 328 TRP ALA ASP LEU VAL HIS PRO ASP ALA GLN ASP ILE LEU SEQRES 25 B 328 ASP THR LEU GLU ASP ASN ARG GLU TRP TYR GLN SER THR SEQRES 26 B 328 ILE PRO GLN HET ZN A 501 1 HET MG A 502 1 HET MKU A 503 30 HET ZN B 501 1 HET MG B 502 1 HET MKU B 503 30 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM MKU 5,9-DIHYDROXY-8-METHOXY-2,2-DIMETHYL-7-(3-METHYLBUT-2- HETNAM 2 MKU EN-1-YL)-3,4-DIHYDRO-2H,6H-PYRANO[3,2-B]XANTHEN-6-ONE HETSYN MKU 3-ISOMANGOSTIN FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 MKU 2(C24 H26 O6) FORMUL 9 HOH *278(H2 O) HELIX 1 AA1 THR A 86 LEU A 96 1 11 HELIX 2 AA2 GLU A 97 VAL A 99 5 3 HELIX 3 AA3 HIS A 105 SER A 113 1 9 HELIX 4 AA4 ARG A 116 ARG A 129 1 14 HELIX 5 AA5 ASP A 130 LYS A 136 1 7 HELIX 6 AA6 PRO A 138 HIS A 152 1 15 HELIX 7 AA7 ASN A 161 SER A 177 1 17 HELIX 8 AA8 THR A 178 GLU A 182 5 5 HELIX 9 AA9 THR A 186 HIS A 200 1 15 HELIX 10 AB1 SER A 208 THR A 215 1 8 HELIX 11 AB2 SER A 217 ASN A 224 1 8 HELIX 12 AB3 SER A 227 LEU A 240 1 14 HELIX 13 AB4 LEU A 241 GLU A 243 5 3 HELIX 14 AB5 THR A 253 ALA A 270 1 18 HELIX 15 AB6 THR A 271 SER A 274 5 4 HELIX 16 AB7 LYS A 275 THR A 289 1 15 HELIX 17 AB8 ASN A 302 LEU A 319 1 18 HELIX 18 AB9 SER A 320 LYS A 324 5 5 HELIX 19 AC1 PRO A 325 ARG A 350 1 26 HELIX 20 AC2 SER A 364 ILE A 376 1 13 HELIX 21 AC3 ILE A 376 VAL A 388 1 13 HELIX 22 AC4 ALA A 392 ILE A 410 1 19 HELIX 23 AC5 THR B 86 GLU B 97 1 12 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 THR B 409 1 18 LINK NE2 HIS A 164 ZN ZN A 501 1555 1555 2.23 LINK NE2 HIS A 200 ZN ZN A 501 1555 1555 2.15 LINK OD2 ASP A 201 ZN ZN A 501 1555 1555 2.24 LINK OD1 ASP A 201 MG MG A 502 1555 1555 2.13 LINK OD1 ASP A 318 ZN ZN A 501 1555 1555 2.16 LINK ZN ZN A 501 O HOH A 635 1555 1555 2.16 LINK ZN ZN A 501 O HOH A 693 1555 1555 2.13 LINK MG MG A 502 O HOH A 635 1555 1555 2.06 LINK MG MG A 502 O HOH A 636 1555 1555 2.20 LINK MG MG A 502 O HOH A 648 1555 1555 2.20 LINK MG MG A 502 O HOH A 659 1555 1555 2.13 LINK MG MG A 502 O HOH A 689 1555 1555 2.12 LINK NE2 HIS B 164 ZN ZN B 501 1555 1555 2.27 LINK NE2 HIS B 200 ZN ZN B 501 1555 1555 2.21 LINK OD2 ASP B 201 ZN ZN B 501 1555 1555 2.10 LINK OD1 ASP B 201 MG MG B 502 1555 1555 2.03 LINK OD2 ASP B 318 ZN ZN B 501 1555 1555 2.01 LINK ZN ZN B 501 O HOH B 634 1555 1555 2.37 LINK ZN ZN B 501 O HOH B 639 1555 1555 2.07 LINK MG MG B 502 O HOH B 612 1555 1555 1.99 LINK MG MG B 502 O HOH B 614 1555 1555 2.07 LINK MG MG B 502 O HOH B 639 1555 1555 1.95 LINK MG MG B 502 O HOH B 652 1555 1555 2.21 LINK MG MG B 502 O HOH B 670 1555 1555 2.21 CISPEP 1 HIS A 389 PRO A 390 0 4.64 CISPEP 2 HIS B 389 PRO B 390 0 -0.34 CISPEP 3 PRO B 411 GLN B 412 0 16.76 SITE 1 AC1 7 HIS A 164 HIS A 200 ASP A 201 ASP A 318 SITE 2 AC1 7 MG A 502 HOH A 635 HOH A 693 SITE 1 AC2 7 ASP A 201 ZN A 501 HOH A 635 HOH A 636 SITE 2 AC2 7 HOH A 648 HOH A 659 HOH A 689 SITE 1 AC3 8 MET A 273 PRO A 322 TRP A 332 ILE A 336 SITE 2 AC3 8 PRO A 356 MET A 357 GLN A 369 PHE A 372 SITE 1 AC4 7 HIS B 164 HIS B 200 ASP B 201 ASP B 318 SITE 2 AC4 7 MG B 502 HOH B 634 HOH B 639 SITE 1 AC5 7 ASP B 201 ZN B 501 HOH B 612 HOH B 614 SITE 2 AC5 7 HOH B 639 HOH B 652 HOH B 670 SITE 1 AC6 9 MET B 273 ASN B 321 PRO B 322 THR B 333 SITE 2 AC6 9 ILE B 336 MET B 357 GLN B 369 PHE B 372 SITE 3 AC6 9 HOH B 656 CRYST1 59.311 79.700 163.316 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 0.016860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006123 0.00000