PDB Short entry for 3WD9 HEADER HYDROLASE/HYDROLASE INHIBITOR 11-JUN-13 3WD9 TITLE CRYSTAL STRUCTURE OF PHOSPHODIESTERASE 4B IN COMPLEX WITH COMPOUND 10F COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 324-700; COMPND 5 SYNONYM: DPDE4, PDE32; 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: DPDE4, PDE4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS PHOSPHODIESTERASE, COPD, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.TAKAHASHI,H.HANZAWA REVDAT 3 08-NOV-23 3WD9 1 REMARK LINK REVDAT 2 22-NOV-17 3WD9 1 REMARK REVDAT 1 23-OCT-13 3WD9 0 JRNL AUTH T.GOTO,A.SHIINA,T.YOSHINO,K.MIZUKAMI,K.HIRAHARA,O.SUZUKI, JRNL AUTH 2 Y.SOGAWA,T.TAKAHASHI,T.MIKKAICHI,N.NAKAO,M.TAKAHASHI, JRNL AUTH 3 M.HASEGAWA,S.SASAKI JRNL TITL SYNTHESIS AND BIOLOGICAL EVALUATION OF JRNL TITL 2 5-CARBAMOYL-2-PHENYLPYRIMIDINE DERIVATIVES AS NOVEL AND JRNL TITL 3 POTENT PDE4 INHIBITORS JRNL REF BIOORG.MED.CHEM. V. 21 7025 2013 JRNL REFN ISSN 0968-0896 JRNL PMID 24094436 JRNL DOI 10.1016/J.BMC.2013.09.013 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 24004 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 + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2400 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1383 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.4160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5584 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 341 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.377 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.245 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.157 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5766 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7814 ; 1.305 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 686 ; 5.449 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 290 ;36.150 ;25.034 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1018 ;17.744 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;22.039 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 874 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4432 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3WD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000096189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: 3W5E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-20% PEG 3350, 0.2-0.4M CACL2, 0.1M REMARK 280 TRIS/HCL (PH8.0), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.65250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 78.68800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.65250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 78.68800 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 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 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 SER A 152 REMARK 465 ILE A 153 REMARK 465 GLN A 486 REMARK 465 SER A 487 REMARK 465 PRO A 488 REMARK 465 SER A 489 REMARK 465 PRO A 490 REMARK 465 PRO A 491 REMARK 465 LEU A 492 REMARK 465 ASP A 493 REMARK 465 GLU A 494 REMARK 465 GLN A 495 REMARK 465 ASN A 496 REMARK 465 ARG A 497 REMARK 465 ASP A 498 REMARK 465 LEU A 512 REMARK 465 ASP A 513 REMARK 465 GLU A 514 REMARK 465 GLU A 515 REMARK 465 ASP A 516 REMARK 465 SER A 517 REMARK 465 GLU A 518 REMARK 465 GLY A 519 REMARK 465 PRO A 520 REMARK 465 GLU A 521 REMARK 465 LYS A 522 REMARK 465 GLU A 523 REMARK 465 GLY A 524 REMARK 465 GLU A 525 REMARK 465 GLY A 526 REMARK 465 HIS A 527 REMARK 465 SER A 528 REMARK 465 SER B 152 REMARK 465 ILE B 153 REMARK 465 GLN B 486 REMARK 465 SER B 487 REMARK 465 PRO B 488 REMARK 465 SER B 489 REMARK 465 PRO B 490 REMARK 465 PRO B 491 REMARK 465 LEU B 492 REMARK 465 ASP B 493 REMARK 465 GLU B 494 REMARK 465 GLN B 495 REMARK 465 ASN B 496 REMARK 465 ARG B 497 REMARK 465 ASP B 498 REMARK 465 LEU B 512 REMARK 465 ASP B 513 REMARK 465 GLU B 514 REMARK 465 GLU B 515 REMARK 465 ASP B 516 REMARK 465 SER B 517 REMARK 465 GLU B 518 REMARK 465 GLY B 519 REMARK 465 PRO B 520 REMARK 465 GLU B 521 REMARK 465 LYS B 522 REMARK 465 GLU B 523 REMARK 465 GLY B 524 REMARK 465 GLU B 525 REMARK 465 GLY B 526 REMARK 465 HIS B 527 REMARK 465 SER B 528 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 OE2 GLU A 421 O HOH A 1039 2.11 REMARK 500 NE2 GLN A 417 O HOH A 1039 2.12 REMARK 500 NE ARG B 331 O HOH B 1014 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 ASN A 235 -162.40 -115.27 REMARK 500 GLU A 427 -132.92 21.06 REMARK 500 SER A 429 98.88 -69.93 REMARK 500 ILE A 450 -60.09 -130.04 REMARK 500 GLN A 463 127.87 -38.44 REMARK 500 LEU B 393 47.09 -102.37 REMARK 500 ILE B 450 -66.65 -122.22 REMARK 500 LEU B 510 97.68 -51.93 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 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 238 NE2 REMARK 620 2 HIS A 274 NE2 97.3 REMARK 620 3 ASP A 275 OD2 93.1 84.4 REMARK 620 4 ASP A 392 OD1 88.9 85.2 169.6 REMARK 620 5 HOH A1004 O 163.0 95.9 98.8 81.6 REMARK 620 6 HOH A1007 O 98.4 164.3 96.5 93.3 68.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 275 OD1 REMARK 620 2 HOH A1001 O 88.1 REMARK 620 3 HOH A1002 O 86.7 88.0 REMARK 620 4 HOH A1003 O 157.8 73.4 80.6 REMARK 620 5 HOH A1004 O 88.6 176.5 90.7 109.6 REMARK 620 6 HOH A1006 O 93.6 78.4 166.4 94.6 103.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 238 NE2 REMARK 620 2 HIS B 274 NE2 91.7 REMARK 620 3 ASP B 275 OD2 89.0 88.7 REMARK 620 4 ASP B 392 OD1 88.3 88.6 176.2 REMARK 620 5 HOH B1004 O 92.7 174.1 95.3 87.5 REMARK 620 6 HOH B1006 O 169.3 98.8 93.0 90.1 76.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 275 OD1 REMARK 620 2 HOH B1001 O 92.8 REMARK 620 3 HOH B1002 O 71.3 100.2 REMARK 620 4 HOH B1003 O 168.9 83.4 99.0 REMARK 620 5 HOH B1005 O 95.6 92.4 162.0 95.0 REMARK 620 6 HOH B1006 O 89.3 174.1 85.7 95.5 81.9 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 QPC A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QPC B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 903 DBREF 3WD9 A 152 528 UNP Q07343 PDE4B_HUMAN 324 700 DBREF 3WD9 B 152 528 UNP Q07343 PDE4B_HUMAN 324 700 SEQRES 1 A 377 SER ILE SER ARG PHE GLY VAL ASN THR GLU ASN GLU ASP SEQRES 2 A 377 HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN LYS TRP GLY SEQRES 3 A 377 LEU ASN ILE PHE ASN VAL ALA GLY TYR SER HIS ASN ARG SEQRES 4 A 377 PRO LEU THR CYS ILE MET TYR ALA ILE PHE GLN GLU ARG SEQRES 5 A 377 ASP LEU LEU LYS THR PHE ARG ILE SER SER ASP THR PHE SEQRES 6 A 377 ILE THR TYR MET MET THR LEU GLU ASP HIS TYR HIS SER SEQRES 7 A 377 ASP VAL ALA TYR HIS ASN SER LEU HIS ALA ALA ASP VAL SEQRES 8 A 377 ALA GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 A 377 ASP ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 A 377 PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 A 377 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 A 377 LEU MET TYR ASN ASP GLU SER VAL LEU GLU ASN HIS HIS SEQRES 13 A 377 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU HIS CYS SEQRES 14 A 377 ASP ILE PHE MET ASN LEU THR LYS LYS GLN ARG GLN THR SEQRES 15 A 377 LEU ARG LYS MET VAL ILE ASP MET VAL LEU ALA THR ASP SEQRES 16 A 377 MET SER LYS HIS MET SER LEU LEU ALA ASP LEU LYS THR SEQRES 17 A 377 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 A 377 LEU LEU ASP ASN TYR THR ASP ARG ILE GLN VAL LEU ARG SEQRES 19 A 377 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 A 377 SER LEU GLU LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 A 377 GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU ARG GLU ARG SEQRES 22 A 377 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS THR ALA SEQRES 23 A 377 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 A 377 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL GLN SEQRES 25 A 377 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 A 377 ARG ASN TRP TYR GLN SER MET ILE PRO GLN SER PRO SER SEQRES 27 A 377 PRO PRO LEU ASP GLU GLN ASN ARG ASP CYS GLN GLY LEU SEQRES 28 A 377 MET GLU LYS PHE GLN PHE GLU LEU THR LEU ASP GLU GLU SEQRES 29 A 377 ASP SER GLU GLY PRO GLU LYS GLU GLY GLU GLY HIS SER SEQRES 1 B 377 SER ILE SER ARG PHE GLY VAL ASN THR GLU ASN GLU ASP SEQRES 2 B 377 HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN LYS TRP GLY SEQRES 3 B 377 LEU ASN ILE PHE ASN VAL ALA GLY TYR SER HIS ASN ARG SEQRES 4 B 377 PRO LEU THR CYS ILE MET TYR ALA ILE PHE GLN GLU ARG SEQRES 5 B 377 ASP LEU LEU LYS THR PHE ARG ILE SER SER ASP THR PHE SEQRES 6 B 377 ILE THR TYR MET MET THR LEU GLU ASP HIS TYR HIS SER SEQRES 7 B 377 ASP VAL ALA TYR HIS ASN SER LEU HIS ALA ALA ASP VAL SEQRES 8 B 377 ALA GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 B 377 ASP ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 B 377 PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 B 377 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 B 377 LEU MET TYR ASN ASP GLU SER VAL LEU GLU ASN HIS HIS SEQRES 13 B 377 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU HIS CYS SEQRES 14 B 377 ASP ILE PHE MET ASN LEU THR LYS LYS GLN ARG GLN THR SEQRES 15 B 377 LEU ARG LYS MET VAL ILE ASP MET VAL LEU ALA THR ASP SEQRES 16 B 377 MET SER LYS HIS MET SER LEU LEU ALA ASP LEU LYS THR SEQRES 17 B 377 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 B 377 LEU LEU ASP ASN TYR THR ASP ARG ILE GLN VAL LEU ARG SEQRES 19 B 377 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 B 377 SER LEU GLU LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 B 377 GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU ARG GLU ARG SEQRES 22 B 377 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS THR ALA SEQRES 23 B 377 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 B 377 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL GLN SEQRES 25 B 377 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 B 377 ARG ASN TRP TYR GLN SER MET ILE PRO GLN SER PRO SER SEQRES 27 B 377 PRO PRO LEU ASP GLU GLN ASN ARG ASP CYS GLN GLY LEU SEQRES 28 B 377 MET GLU LYS PHE GLN PHE GLU LEU THR LEU ASP GLU GLU SEQRES 29 B 377 ASP SER GLU GLY PRO GLU LYS GLU GLY GLU GLY HIS SER HET QPC A 901 31 HET ZN A 902 1 HET CA A 903 1 HET QPC B 901 31 HET ZN B 902 1 HET CA B 903 1 HETNAM QPC 4-[(4-{2-[(2,2-DIMETHYLPROPYL)AMINO]-2- HETNAM 2 QPC OXOETHYL}PHENYL)AMINO]-2-PHENYLPYRIMIDINE-5- HETNAM 3 QPC CARBOXAMIDE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 QPC 2(C24 H27 N5 O2) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 CA 2(CA 2+) FORMUL 9 HOH *341(H2 O) HELIX 1 1 ASN A 162 LEU A 170 1 9 HELIX 2 2 GLU A 171 LEU A 173 5 3 HELIX 3 3 ASN A 179 HIS A 188 1 10 HELIX 4 4 ARG A 190 ARG A 203 1 14 HELIX 5 5 ASP A 204 PHE A 209 1 6 HELIX 6 6 SER A 212 HIS A 226 1 15 HELIX 7 7 ASN A 235 LEU A 250 1 16 HELIX 8 8 THR A 260 HIS A 274 1 15 HELIX 9 9 SER A 282 THR A 289 1 8 HELIX 10 10 SER A 291 TYR A 297 1 7 HELIX 11 11 SER A 301 LEU A 314 1 14 HELIX 12 12 LEU A 315 GLU A 317 5 3 HELIX 13 13 THR A 327 THR A 345 1 19 HELIX 14 14 ASP A 346 SER A 348 5 3 HELIX 15 15 LYS A 349 THR A 363 1 15 HELIX 16 16 ASN A 376 LEU A 393 1 18 HELIX 17 17 SER A 394 LYS A 398 5 5 HELIX 18 18 SER A 399 ARG A 424 1 26 HELIX 19 19 SER A 438 ILE A 450 1 13 HELIX 20 20 ILE A 450 VAL A 462 1 13 HELIX 21 21 ALA A 466 MET A 483 1 18 HELIX 22 22 GLY A 501 GLU A 509 1 9 HELIX 23 23 GLU B 161 LEU B 170 1 10 HELIX 24 24 GLU B 171 LEU B 173 5 3 HELIX 25 25 ASN B 179 SER B 187 1 9 HELIX 26 26 ARG B 190 ARG B 203 1 14 HELIX 27 27 ASP B 204 PHE B 209 1 6 HELIX 28 28 SER B 212 HIS B 226 1 15 HELIX 29 29 ASN B 235 SER B 251 1 17 HELIX 30 30 THR B 252 ASP B 256 5 5 HELIX 31 31 THR B 260 HIS B 274 1 15 HELIX 32 32 SER B 282 THR B 289 1 8 HELIX 33 33 SER B 291 TYR B 297 1 7 HELIX 34 34 SER B 301 LEU B 314 1 14 HELIX 35 35 LEU B 315 GLU B 317 5 3 HELIX 36 36 THR B 327 ALA B 344 1 18 HELIX 37 37 THR B 345 SER B 348 5 4 HELIX 38 38 LYS B 349 GLU B 362 1 14 HELIX 39 39 ASN B 376 LEU B 393 1 18 HELIX 40 40 SER B 394 LYS B 398 5 5 HELIX 41 41 SER B 399 ARG B 424 1 26 HELIX 42 42 SER B 438 ILE B 450 1 13 HELIX 43 43 ILE B 450 GLN B 463 1 14 HELIX 44 44 ALA B 466 MET B 483 1 18 HELIX 45 45 GLY B 501 LEU B 510 1 10 SSBOND 1 CYS A 432 CYS A 499 1555 1555 2.05 SSBOND 2 CYS B 432 CYS B 499 1555 1555 2.05 LINK NE2 HIS A 238 ZN ZN A 902 1555 1555 2.21 LINK NE2 HIS A 274 ZN ZN A 902 1555 1555 2.37 LINK OD2 ASP A 275 ZN ZN A 902 1555 1555 2.07 LINK OD1 ASP A 275 CA CA A 903 1555 1555 2.56 LINK OD1 ASP A 392 ZN ZN A 902 1555 1555 2.32 LINK ZN ZN A 902 O HOH A1004 1555 1555 1.73 LINK ZN ZN A 902 O HOH A1007 1555 1555 2.44 LINK CA CA A 903 O HOH A1001 1555 1555 2.77 LINK CA CA A 903 O HOH A1002 1555 1555 2.64 LINK CA CA A 903 O HOH A1003 1555 1555 2.40 LINK CA CA A 903 O HOH A1004 1555 1555 2.52 LINK CA CA A 903 O HOH A1006 1555 1555 2.50 LINK NE2 HIS B 238 ZN ZN B 902 1555 1555 2.21 LINK NE2 HIS B 274 ZN ZN B 902 1555 1555 2.20 LINK OD2 ASP B 275 ZN ZN B 902 1555 1555 2.30 LINK OD1 ASP B 275 CA CA B 903 1555 1555 2.39 LINK OD1 ASP B 392 ZN ZN B 902 1555 1555 2.35 LINK ZN ZN B 902 O HOH B1004 1555 1555 2.43 LINK ZN ZN B 902 O HOH B1006 1555 1555 2.04 LINK CA CA B 903 O HOH B1001 1555 1555 2.33 LINK CA CA B 903 O HOH B1002 1555 1555 2.49 LINK CA CA B 903 O HOH B1003 1555 1555 2.48 LINK CA CA B 903 O HOH B1005 1555 1555 2.56 LINK CA CA B 903 O HOH B1006 1555 1555 2.49 CISPEP 1 GLN A 463 PRO A 464 0 -4.38 CISPEP 2 GLN B 463 PRO B 464 0 1.92 SITE 1 AC1 16 TYR A 233 SER A 282 ASN A 395 PHE A 414 SITE 2 AC1 16 SER A 442 GLN A 443 PHE A 446 LEU A 502 SITE 3 AC1 16 MET A 503 PHE A 506 GLU A 509 HOH A1055 SITE 4 AC1 16 HOH A1093 HOH A1111 HOH A1121 HOH A1153 SITE 1 AC2 6 HIS A 238 HIS A 274 ASP A 275 ASP A 392 SITE 2 AC2 6 HOH A1004 HOH A1007 SITE 1 AC3 6 ASP A 275 HOH A1001 HOH A1002 HOH A1003 SITE 2 AC3 6 HOH A1004 HOH A1006 SITE 1 AC4 17 TYR B 233 GLY B 280 VAL B 281 SER B 282 SITE 2 AC4 17 ASN B 395 ILE B 410 GLU B 413 PHE B 414 SITE 3 AC4 17 GLN B 417 SER B 442 GLN B 443 PHE B 446 SITE 4 AC4 17 LEU B 502 HOH B1040 HOH B1053 HOH B1077 SITE 5 AC4 17 HOH B1176 SITE 1 AC5 6 HIS B 238 HIS B 274 ASP B 275 ASP B 392 SITE 2 AC5 6 HOH B1004 HOH B1006 SITE 1 AC6 6 ASP B 275 HOH B1001 HOH B1002 HOH B1003 SITE 2 AC6 6 HOH B1005 HOH B1006 CRYST1 81.305 157.376 58.050 90.00 90.00 90.00 P 21 21 2 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 0.012299 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017227 0.00000