HEADER HYDROLASE 03-MAY-05 1ZKN TITLE STRUCTURE OF PDE4D2-IBMX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: DPDE3, PDE43; COMPND 6 EC: 3.1.4.17; COMPND 7 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PROTEIN-INHIBITOR COMPLEX, INHIBITOR SELECTIVITY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.HUAI,Y.LIU,S.H.FRANCIS,J.D.CORBIN,H.KE REVDAT 4 03-APR-24 1ZKN 1 REMARK REVDAT 3 14-FEB-24 1ZKN 1 REMARK LINK REVDAT 2 24-FEB-09 1ZKN 1 VERSN REVDAT 1 17-MAY-05 1ZKN 0 SPRSDE 17-MAY-05 1ZKN 1RKO JRNL AUTH Q.HUAI,Y.LIU,S.H.FRANCIS,J.D.CORBIN,H.KE JRNL TITL CRYSTAL STRUCTURES OF PHOSPHODIESTERASES 4 AND 5 IN COMPLEX JRNL TITL 2 WITH INHIBITOR 3-ISOBUTYL-1-METHYLXANTHINE SUGGEST A JRNL TITL 3 CONFORMATION DETERMINANT OF INHIBITOR SELECTIVITY JRNL REF J.BIOL.CHEM. V. 279 13095 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14668322 JRNL DOI 10.1074/JBC.M311556200 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 89970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 9019 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 10726 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.80 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.090 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : 0.44000 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDE4D2 CATALYTIC DOMAIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50 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 49.85200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.69350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.85150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.69350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.85200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.85150 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 ILE C 79 REMARK 465 PRO C 80 REMARK 465 ARG C 81 REMARK 465 PHE C 82 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 161 -167.44 -126.36 REMARK 500 ASP A 225 14.55 54.85 REMARK 500 ASP A 301 -106.16 -68.95 REMARK 500 ASN A 302 165.82 -35.57 REMARK 500 ILE A 376 -65.12 -123.09 REMARK 500 ASN B 161 -165.08 -120.42 REMARK 500 ASN B 362 58.43 -147.85 REMARK 500 ILE B 376 -55.54 -131.04 REMARK 500 PRO B 411 162.70 -49.14 REMARK 500 LYS C 85 69.25 -59.85 REMARK 500 ASN C 161 -167.67 -124.01 REMARK 500 ASP C 225 16.50 52.99 REMARK 500 LYS C 290 103.42 -29.26 REMARK 500 LEU C 326 -38.72 -36.65 REMARK 500 ASN C 362 66.09 -151.48 REMARK 500 ILE C 376 -60.49 -137.38 REMARK 500 PRO C 411 173.51 -56.75 REMARK 500 THR D 86 126.01 178.46 REMARK 500 SER D 227 52.94 39.63 REMARK 500 ILE D 376 -63.53 -121.63 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 164 NE2 REMARK 620 2 HIS A 200 NE2 93.8 REMARK 620 3 ASP A 201 OD2 91.7 81.7 REMARK 620 4 ASP A 318 OD1 86.9 90.8 172.2 REMARK 620 5 HOH A 621 O 92.5 173.1 100.7 87.0 REMARK 620 N 1 2 3 4 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 201 OD1 REMARK 620 2 HOH A 634 O 82.4 REMARK 620 3 HOH A 635 O 169.5 87.1 REMARK 620 4 HOH A 637 O 91.8 95.0 88.5 REMARK 620 N 1 2 3 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 164 NE2 REMARK 620 2 HIS B 200 NE2 103.6 REMARK 620 3 ASP B 201 OD2 93.0 88.2 REMARK 620 4 ASP B 318 OD1 85.6 83.9 171.4 REMARK 620 5 HOH B 624 O 91.3 164.6 95.1 93.4 REMARK 620 N 1 2 3 4 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 201 OD1 REMARK 620 2 HOH B 606 O 70.5 REMARK 620 3 HOH B 625 O 149.4 79.4 REMARK 620 4 HOH B 627 O 89.6 85.2 82.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 164 NE2 REMARK 620 2 HIS C 200 NE2 96.8 REMARK 620 3 ASP C 201 OD2 90.2 82.3 REMARK 620 4 ASP C 318 OD1 89.7 88.3 170.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 201 OD1 REMARK 620 2 HOH C 611 O 165.9 REMARK 620 3 HOH C 616 O 85.6 83.6 REMARK 620 4 HOH C 621 O 82.7 87.1 83.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 164 NE2 REMARK 620 2 HIS D 200 NE2 105.4 REMARK 620 3 ASP D 201 OD2 90.4 84.7 REMARK 620 4 ASP D 318 OD1 86.9 91.4 174.5 REMARK 620 5 HOH D 639 O 160.1 93.6 97.1 87.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 201 OD1 REMARK 620 2 HOH D 618 O 89.2 REMARK 620 3 HOH D 629 O 166.9 77.8 REMARK 620 4 HOH D 639 O 96.3 167.4 96.6 REMARK 620 5 HOH D 640 O 87.5 92.0 92.2 99.5 REMARK 620 N 1 2 3 4 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 ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM C 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IBM D 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RKO RELATED DB: PDB REMARK 900 THE NEW DEPOSIT IS TO REPLACE 1RKO DBREF 1ZKN A 79 412 UNP Q08499 PDE4D_HUMAN 381 714 DBREF 1ZKN B 79 412 UNP Q08499 PDE4D_HUMAN 381 714 DBREF 1ZKN C 79 412 UNP Q08499 PDE4D_HUMAN 381 714 DBREF 1ZKN D 79 412 UNP Q08499 PDE4D_HUMAN 381 714 SEQRES 1 A 334 ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP VAL SEQRES 2 A 334 LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY LEU SEQRES 3 A 334 HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG PRO SEQRES 4 A 334 LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG ASP SEQRES 5 A 334 LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU ILE SEQRES 6 A 334 THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA ASP SEQRES 7 A 334 VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL VAL SEQRES 8 A 334 GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU GLU SEQRES 9 A 334 ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE PHE SEQRES 10 A 334 ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SER SEQRES 11 A 334 ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA LEU SEQRES 12 A 334 MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS LEU SEQRES 13 A 334 ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS ASP SEQRES 14 A 334 ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER LEU SEQRES 15 A 334 ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP MET SEQRES 16 A 334 SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR MET SEQRES 17 A 334 VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU LEU SEQRES 18 A 334 LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN ASN SEQRES 19 A 334 MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS PRO SEQRES 20 A 334 LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET GLU SEQRES 21 A 334 GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG GLY SEQRES 22 A 334 MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SER SEQRES 23 A 334 VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE VAL SEQRES 24 A 334 HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS PRO SEQRES 25 A 334 ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN ARG SEQRES 26 A 334 GLU TRP TYR GLN SER THR ILE PRO GLN SEQRES 1 B 334 ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP VAL SEQRES 2 B 334 LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY LEU SEQRES 3 B 334 HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG PRO SEQRES 4 B 334 LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG ASP SEQRES 5 B 334 LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU ILE SEQRES 6 B 334 THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA ASP SEQRES 7 B 334 VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL VAL SEQRES 8 B 334 GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU GLU SEQRES 9 B 334 ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE PHE SEQRES 10 B 334 ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SER SEQRES 11 B 334 ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA LEU SEQRES 12 B 334 MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS LEU SEQRES 13 B 334 ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS ASP SEQRES 14 B 334 ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER LEU SEQRES 15 B 334 ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP MET SEQRES 16 B 334 SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR MET SEQRES 17 B 334 VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU LEU SEQRES 18 B 334 LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN ASN SEQRES 19 B 334 MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS PRO SEQRES 20 B 334 LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET GLU SEQRES 21 B 334 GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG GLY SEQRES 22 B 334 MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SER SEQRES 23 B 334 VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE VAL SEQRES 24 B 334 HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS PRO SEQRES 25 B 334 ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN ARG SEQRES 26 B 334 GLU TRP TYR GLN SER THR ILE PRO GLN SEQRES 1 C 334 ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP VAL SEQRES 2 C 334 LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY LEU SEQRES 3 C 334 HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG PRO SEQRES 4 C 334 LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG ASP SEQRES 5 C 334 LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU ILE SEQRES 6 C 334 THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA ASP SEQRES 7 C 334 VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL VAL SEQRES 8 C 334 GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU GLU SEQRES 9 C 334 ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE PHE SEQRES 10 C 334 ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SER SEQRES 11 C 334 ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA LEU SEQRES 12 C 334 MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS LEU SEQRES 13 C 334 ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS ASP SEQRES 14 C 334 ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER LEU SEQRES 15 C 334 ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP MET SEQRES 16 C 334 SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR MET SEQRES 17 C 334 VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU LEU SEQRES 18 C 334 LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN ASN SEQRES 19 C 334 MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS PRO SEQRES 20 C 334 LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET GLU SEQRES 21 C 334 GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG GLY SEQRES 22 C 334 MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SER SEQRES 23 C 334 VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE VAL SEQRES 24 C 334 HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS PRO SEQRES 25 C 334 ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN ARG SEQRES 26 C 334 GLU TRP TYR GLN SER THR ILE PRO GLN SEQRES 1 D 334 ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP VAL SEQRES 2 D 334 LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY LEU SEQRES 3 D 334 HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG PRO SEQRES 4 D 334 LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG ASP SEQRES 5 D 334 LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU ILE SEQRES 6 D 334 THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA ASP SEQRES 7 D 334 VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL VAL SEQRES 8 D 334 GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU GLU SEQRES 9 D 334 ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE PHE SEQRES 10 D 334 ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SER SEQRES 11 D 334 ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA LEU SEQRES 12 D 334 MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS LEU SEQRES 13 D 334 ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS ASP SEQRES 14 D 334 ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER LEU SEQRES 15 D 334 ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP MET SEQRES 16 D 334 SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR MET SEQRES 17 D 334 VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU LEU SEQRES 18 D 334 LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN ASN SEQRES 19 D 334 MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS PRO SEQRES 20 D 334 LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET GLU SEQRES 21 D 334 GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG GLY SEQRES 22 D 334 MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SER SEQRES 23 D 334 VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE VAL SEQRES 24 D 334 HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS PRO SEQRES 25 D 334 ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN ARG SEQRES 26 D 334 GLU TRP TYR GLN SER THR ILE PRO GLN HET ZN A 601 1 HET MG A 602 1 HET IBM A 603 16 HET ZN B 601 1 HET MG B 602 1 HET IBM B 603 16 HET ZN C 601 1 HET MG C 602 1 HET IBM C 603 16 HET ZN D 601 1 HET MG D 602 1 HET IBM D 501 16 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM IBM 3-ISOBUTYL-1-METHYLXANTHINE FORMUL 5 ZN 4(ZN 2+) FORMUL 6 MG 4(MG 2+) FORMUL 7 IBM 4(C10 H14 N4 O2) FORMUL 17 HOH *189(H2 O) HELIX 1 1 THR A 86 LEU A 96 1 11 HELIX 2 2 GLU A 97 VAL A 99 5 3 HELIX 3 3 HIS A 105 SER A 113 1 9 HELIX 4 4 ARG A 116 ARG A 129 1 14 HELIX 5 5 ASP A 130 PHE A 135 1 6 HELIX 6 6 PRO A 138 HIS A 152 1 15 HELIX 7 7 ASN A 161 SER A 177 1 17 HELIX 8 8 THR A 178 GLU A 182 5 5 HELIX 9 9 THR A 186 HIS A 200 1 15 HELIX 10 10 SER A 208 THR A 215 1 8 HELIX 11 11 SER A 217 TYR A 223 1 7 HELIX 12 12 SER A 227 LEU A 240 1 14 HELIX 13 13 LEU A 241 GLU A 243 5 3 HELIX 14 14 THR A 253 ALA A 270 1 18 HELIX 15 15 THR A 271 SER A 274 5 4 HELIX 16 16 LYS A 275 THR A 289 1 15 HELIX 17 17 ASN A 302 LEU A 319 1 18 HELIX 18 18 SER A 320 LYS A 324 5 5 HELIX 19 19 PRO A 325 ARG A 350 1 26 HELIX 20 20 SER A 364 ILE A 376 1 13 HELIX 21 21 ILE A 376 VAL A 388 1 13 HELIX 22 22 ALA A 392 ILE A 410 1 19 HELIX 23 23 THR B 86 LEU B 96 1 11 HELIX 24 24 GLU B 97 VAL B 99 5 3 HELIX 25 25 HIS B 105 SER B 113 1 9 HELIX 26 26 ARG B 116 ARG B 129 1 14 HELIX 27 27 ASP B 130 PHE B 135 1 6 HELIX 28 28 PRO B 138 HIS B 152 1 15 HELIX 29 29 ASN B 161 SER B 177 1 17 HELIX 30 30 THR B 178 GLU B 182 5 5 HELIX 31 31 THR B 186 HIS B 200 1 15 HELIX 32 32 SER B 208 THR B 215 1 8 HELIX 33 33 SER B 217 ASN B 224 1 8 HELIX 34 34 SER B 227 LEU B 240 1 14 HELIX 35 35 LEU B 241 GLU B 243 5 3 HELIX 36 36 THR B 253 ALA B 270 1 18 HELIX 37 37 LYS B 275 THR B 289 1 15 HELIX 38 38 ASN B 302 LEU B 319 1 18 HELIX 39 39 SER B 320 LYS B 324 5 5 HELIX 40 40 PRO B 325 GLY B 351 1 27 HELIX 41 41 SER B 364 ILE B 376 1 13 HELIX 42 42 ILE B 376 VAL B 388 1 13 HELIX 43 43 ALA B 392 SER B 408 1 17 HELIX 44 44 THR C 86 LEU C 96 1 11 HELIX 45 45 GLU C 97 LYS C 101 5 5 HELIX 46 46 HIS C 105 SER C 113 1 9 HELIX 47 47 ARG C 116 ARG C 129 1 14 HELIX 48 48 ASP C 130 PHE C 135 1 6 HELIX 49 49 PRO C 138 HIS C 152 1 15 HELIX 50 50 ASN C 161 SER C 177 1 17 HELIX 51 51 THR C 178 GLU C 182 5 5 HELIX 52 52 THR C 186 HIS C 200 1 15 HELIX 53 53 SER C 208 THR C 215 1 8 HELIX 54 54 SER C 217 ASN C 224 1 8 HELIX 55 55 SER C 227 LEU C 240 1 14 HELIX 56 56 LEU C 241 GLU C 243 5 3 HELIX 57 57 THR C 253 ALA C 270 1 18 HELIX 58 58 THR C 271 SER C 274 5 4 HELIX 59 59 LYS C 275 GLU C 288 1 14 HELIX 60 60 ASN C 302 LEU C 319 1 18 HELIX 61 61 SER C 320 LYS C 324 5 5 HELIX 62 62 PRO C 325 GLY C 351 1 27 HELIX 63 63 SER C 364 ILE C 376 1 13 HELIX 64 64 ILE C 376 VAL C 388 1 13 HELIX 65 65 ALA C 392 SER C 408 1 17 HELIX 66 66 GLN D 88 GLU D 97 1 10 HELIX 67 67 HIS D 105 SER D 113 1 9 HELIX 68 68 ARG D 116 ARG D 129 1 14 HELIX 69 69 ASP D 130 PHE D 135 1 6 HELIX 70 70 PRO D 138 HIS D 152 1 15 HELIX 71 71 ASN D 161 SER D 177 1 17 HELIX 72 72 THR D 178 GLU D 182 5 5 HELIX 73 73 THR D 186 HIS D 200 1 15 HELIX 74 74 SER D 208 THR D 215 1 8 HELIX 75 75 SER D 217 TYR D 223 1 7 HELIX 76 76 SER D 227 LEU D 240 1 14 HELIX 77 77 LEU D 241 GLU D 243 5 3 HELIX 78 78 THR D 253 ALA D 270 1 18 HELIX 79 79 THR D 271 SER D 274 5 4 HELIX 80 80 LYS D 275 THR D 289 1 15 HELIX 81 81 ASN D 302 LEU D 319 1 18 HELIX 82 82 SER D 320 LYS D 324 5 5 HELIX 83 83 PRO D 325 ARG D 350 1 26 HELIX 84 84 SER D 364 ILE D 376 1 13 HELIX 85 85 ILE D 376 VAL D 388 1 13 HELIX 86 86 ALA D 392 SER D 408 1 17 LINK NE2 HIS A 164 ZN ZN A 601 1555 1555 2.11 LINK NE2 HIS A 200 ZN ZN A 601 1555 1555 2.11 LINK OD2 ASP A 201 ZN ZN A 601 1555 1555 2.06 LINK OD1 ASP A 201 MG MG A 602 1555 1555 2.40 LINK OD1 ASP A 318 ZN ZN A 601 1555 1555 2.06 LINK ZN ZN A 601 O HOH A 621 1555 1555 2.38 LINK MG MG A 602 O HOH A 634 1555 1555 2.49 LINK MG MG A 602 O HOH A 635 1555 1555 2.34 LINK MG MG A 602 O HOH A 637 1555 1555 2.33 LINK NE2 HIS B 164 ZN ZN B 601 1555 1555 2.11 LINK NE2 HIS B 200 ZN ZN B 601 1555 1555 2.11 LINK OD2 ASP B 201 ZN ZN B 601 1555 1555 2.06 LINK OD1 ASP B 201 MG MG B 602 1555 1555 2.32 LINK OD1 ASP B 318 ZN ZN B 601 1555 1555 2.07 LINK ZN ZN B 601 O HOH B 624 1555 1555 2.35 LINK MG MG B 602 O HOH B 606 1555 1555 2.52 LINK MG MG B 602 O HOH B 625 1555 1555 2.40 LINK MG MG B 602 O HOH B 627 1555 1555 2.48 LINK NE2 HIS C 164 ZN ZN C 601 1555 1555 2.10 LINK NE2 HIS C 200 ZN ZN C 601 1555 1555 2.11 LINK OD2 ASP C 201 ZN ZN C 601 1555 1555 2.05 LINK OD1 ASP C 201 MG MG C 602 1555 1555 2.37 LINK OD1 ASP C 318 ZN ZN C 601 1555 1555 2.07 LINK MG MG C 602 O HOH C 611 1555 1555 2.39 LINK MG MG C 602 O HOH C 616 1555 1555 2.54 LINK MG MG C 602 O HOH C 621 1555 1555 2.36 LINK NE2 HIS D 164 ZN ZN D 601 1555 1555 2.11 LINK NE2 HIS D 200 ZN ZN D 601 1555 1555 2.10 LINK OD2 ASP D 201 ZN ZN D 601 1555 1555 2.06 LINK OD1 ASP D 201 MG MG D 602 1555 1555 2.34 LINK OD1 ASP D 318 ZN ZN D 601 1555 1555 2.07 LINK ZN ZN D 601 O HOH D 639 1555 1555 2.34 LINK MG MG D 602 O HOH D 618 1555 1555 2.49 LINK MG MG D 602 O HOH D 629 1555 1555 2.48 LINK MG MG D 602 O HOH D 639 1555 1555 2.34 LINK MG MG D 602 O HOH D 640 1555 1555 2.34 CISPEP 1 HIS A 389 PRO A 390 0 -0.07 CISPEP 2 HIS B 389 PRO B 390 0 -0.08 CISPEP 3 HIS C 389 PRO C 390 0 0.09 CISPEP 4 HIS D 389 PRO D 390 0 0.08 SITE 1 AC1 5 HIS A 164 HIS A 200 ASP A 201 ASP A 318 SITE 2 AC1 5 HOH A 621 SITE 1 AC2 4 ASP A 201 HOH A 634 HOH A 635 HOH A 637 SITE 1 AC3 5 HIS B 164 HIS B 200 ASP B 201 ASP B 318 SITE 2 AC3 5 HOH B 624 SITE 1 AC4 4 ASP B 201 HOH B 606 HOH B 625 HOH B 627 SITE 1 AC5 4 HIS C 164 HIS C 200 ASP C 201 ASP C 318 SITE 1 AC6 4 ASP C 201 HOH C 611 HOH C 616 HOH C 621 SITE 1 AC7 5 HIS D 164 HIS D 200 ASP D 201 ASP D 318 SITE 2 AC7 5 HOH D 639 SITE 1 AC8 5 ASP D 201 HOH D 618 HOH D 629 HOH D 639 SITE 2 AC8 5 HOH D 640 SITE 1 AC9 5 ILE A 336 PHE A 340 MET A 357 GLN A 369 SITE 2 AC9 5 HOH A 639 SITE 1 BC1 5 MET B 273 PHE B 340 MET B 357 GLN B 369 SITE 2 BC1 5 PHE B 372 SITE 1 BC2 5 MET C 273 ILE C 336 MET C 357 GLN C 369 SITE 2 BC2 5 PHE C 372 SITE 1 BC3 4 MET D 273 MET D 357 GLN D 369 PHE D 372 CRYST1 99.704 111.703 159.387 90.00 90.00 90.00 P 21 21 21 16 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 0.010030 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006274 0.00000