HEADER HYDROLASE 24-MAY-16 5K6J TITLE HUMAN PHOSPODIESTERASE 4B IN COMPLEX WITH PYRIDYLOXY-BENZOXABOROLE TITLE 2 BASED INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 101-423; COMPND 5 SYNONYM: DPDE4,PDE32; COMPND 6 EC: 3.1.4.53; 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: PDE4B, DPDE4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHODIESTERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.L.ROCK,Y.ZHOU,D.SULLIVAN REVDAT 4 06-MAR-24 5K6J 1 LINK REVDAT 3 24-JAN-18 5K6J 1 REMARK REVDAT 2 14-JUN-17 5K6J 1 HETNAM REVDAT 1 31-MAY-17 5K6J 0 JRNL AUTH C.DONG,K.JARNAGIN JRNL TITL TO BE PUBLISHED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27295 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2290 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1717 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2615 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -2.67000 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): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.140 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2801 ; 0.007 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1873 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3773 ; 0.975 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4564 ; 0.982 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 332 ; 4.690 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;31.588 ;24.855 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 488 ;10.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;11.526 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 418 ; 0.050 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3064 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 546 ; 0.001 ; 0.020 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5K6J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 57.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 15.50 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 16.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 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: MOLREP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION : NULL, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 114.92500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.91950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.91950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 172.38750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.91950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.91950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.46250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.91950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.91950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 172.38750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.91950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.91950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 57.46250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 114.92500 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: 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 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 ASP A 299 10.59 58.95 REMARK 500 LEU A 393 38.12 -99.87 REMARK 500 ILE A 450 -60.65 -125.62 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 238 NE2 REMARK 620 2 HIS A 274 NE2 91.0 REMARK 620 3 ASP A 275 OD2 82.8 80.4 REMARK 620 4 ASP A 392 OD1 91.0 89.2 167.8 REMARK 620 5 6QQ A 503 O18 156.7 111.9 96.7 93.1 REMARK 620 6 6QQ A 503 O19 96.8 168.1 91.6 99.6 60.0 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 275 OD1 REMARK 620 2 6QQ A 503 O16 94.0 REMARK 620 3 6QQ A 503 O18 98.6 62.5 REMARK 620 4 HOH A 603 O 85.0 171.2 108.9 REMARK 620 5 HOH A 639 O 172.5 93.5 84.9 87.6 REMARK 620 6 HOH A 662 O 85.9 91.8 154.2 96.8 93.9 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 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 6QQ A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 520 DBREF 5K6J A 162 484 UNP Q07343 PDE4B_HUMAN 101 423 SEQRES 1 A 323 ASN GLU ASP HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN SEQRES 2 A 323 LYS TRP GLY LEU ASN ILE PHE ASN VAL ALA GLY TYR SER SEQRES 3 A 323 HIS ASN ARG PRO LEU THR CYS ILE MET TYR ALA ILE PHE SEQRES 4 A 323 GLN GLU ARG ASP LEU LEU LYS THR PHE ARG ILE SER SER SEQRES 5 A 323 ASP THR PHE ILE THR TYR MET MET THR LEU GLU ASP HIS SEQRES 6 A 323 TYR HIS SER ASP VAL ALA TYR HIS ASN SER LEU HIS ALA SEQRES 7 A 323 ALA ASP VAL ALA GLN SER THR HIS VAL LEU LEU SER THR SEQRES 8 A 323 PRO ALA LEU ASP ALA VAL PHE THR ASP LEU GLU ILE LEU SEQRES 9 A 323 ALA ALA ILE PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS SEQRES 10 A 323 PRO GLY VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER SEQRES 11 A 323 GLU LEU ALA LEU MET TYR ASN ASP GLU SER VAL LEU GLU SEQRES 12 A 323 ASN HIS HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU SEQRES 13 A 323 GLU HIS CYS ASP ILE PHE MET ASN LEU THR LYS LYS GLN SEQRES 14 A 323 ARG GLN THR LEU ARG LYS MET VAL ILE ASP MET VAL LEU SEQRES 15 A 323 ALA THR ASP MET SER LYS HIS MET SER LEU LEU ALA ASP SEQRES 16 A 323 LEU LYS THR MET VAL GLU THR LYS LYS VAL THR SER SER SEQRES 17 A 323 GLY VAL LEU LEU LEU ASP ASN TYR THR ASP ARG ILE GLN SEQRES 18 A 323 VAL LEU ARG ASN MET VAL HIS CYS ALA ASP LEU SER ASN SEQRES 19 A 323 PRO THR LYS SER LEU GLU LEU TYR ARG GLN TRP THR ASP SEQRES 20 A 323 ARG ILE MET GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU SEQRES 21 A 323 ARG GLU ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS SEQRES 22 A 323 HIS THR ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE SEQRES 23 A 323 ASP TYR ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP SEQRES 24 A 323 LEU VAL GLN PRO ASP ALA GLN ASP ILE LEU ASP THR LEU SEQRES 25 A 323 GLU ASP ASN ARG ASN TRP TYR GLN SER MET ILE HET ZN A 501 1 HET MG A 502 1 HET 6QQ A 503 28 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 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 4 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 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 6QQ 6-[[7,7-BIS(OXIDANYL)-8-OXA-7- HETNAM 2 6QQ BORANUIDABICYCLO[4.3.0]NONA-1(6),2,4-TRIEN-3-YL]OXY]- HETNAM 3 6QQ 5-CHLORANYL-2-(4-OXIDANYLIDENEPENTOXY)PYRIDINE-3- HETNAM 4 6QQ CARBONITRILE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 6QQ C18 H17 B CL N2 O6 1- FORMUL 5 EDO 17(C2 H6 O2) FORMUL 22 HOH *139(H2 O) HELIX 1 AA1 ASN A 162 LEU A 170 1 9 HELIX 2 AA2 GLU A 171 LEU A 173 5 3 HELIX 3 AA3 ASN A 179 SER A 187 1 9 HELIX 4 AA4 ARG A 190 ARG A 203 1 14 HELIX 5 AA5 ASP A 204 PHE A 209 1 6 HELIX 6 AA6 SER A 212 HIS A 226 1 15 HELIX 7 AA7 ASN A 235 SER A 251 1 17 HELIX 8 AA8 THR A 252 ASP A 256 5 5 HELIX 9 AA9 THR A 260 HIS A 274 1 15 HELIX 10 AB1 SER A 282 THR A 289 1 8 HELIX 11 AB2 SER A 291 TYR A 297 1 7 HELIX 12 AB3 SER A 301 LEU A 314 1 14 HELIX 13 AB4 LEU A 315 GLU A 317 5 3 HELIX 14 AB5 THR A 327 ALA A 344 1 18 HELIX 15 AB6 THR A 345 SER A 348 5 4 HELIX 16 AB7 LYS A 349 THR A 363 1 15 HELIX 17 AB8 ASN A 376 LEU A 393 1 18 HELIX 18 AB9 SER A 394 LYS A 398 5 5 HELIX 19 AC1 SER A 399 ARG A 424 1 26 HELIX 20 AC2 SER A 438 ILE A 450 1 13 HELIX 21 AC3 ILE A 450 VAL A 462 1 13 HELIX 22 AC4 ALA A 466 MET A 483 1 18 SHEET 1 AA1 2 LYS A 365 VAL A 366 0 SHEET 2 AA1 2 LEU A 372 LEU A 373 -1 O LEU A 373 N LYS A 365 LINK NE2 HIS A 238 ZN ZN A 501 1555 1555 2.19 LINK NE2 HIS A 274 ZN ZN A 501 1555 1555 2.19 LINK OD2 ASP A 275 ZN ZN A 501 1555 1555 2.15 LINK OD1 ASP A 275 MG MG A 502 1555 1555 2.21 LINK OD1 ASP A 392 ZN ZN A 501 1555 1555 2.20 LINK ZN ZN A 501 O18 6QQ A 503 1555 1555 2.25 LINK ZN ZN A 501 O19 6QQ A 503 1555 1555 2.18 LINK MG MG A 502 O16 6QQ A 503 1555 1555 2.20 LINK MG MG A 502 O18 6QQ A 503 1555 1555 2.18 LINK MG MG A 502 O HOH A 603 1555 1555 2.13 LINK MG MG A 502 O HOH A 639 1555 1555 2.00 LINK MG MG A 502 O HOH A 662 1555 1555 2.23 CISPEP 1 GLN A 463 PRO A 464 0 -0.53 SITE 1 AC1 5 HIS A 238 HIS A 274 ASP A 275 ASP A 392 SITE 2 AC1 5 6QQ A 503 SITE 1 AC2 5 ASP A 275 6QQ A 503 HOH A 603 HOH A 639 SITE 2 AC2 5 HOH A 662 SITE 1 AC3 17 HIS A 234 HIS A 238 HIS A 274 ASP A 275 SITE 2 AC3 17 MET A 347 ASP A 392 LEU A 393 ASN A 395 SITE 3 AC3 17 PRO A 396 ILE A 410 MET A 431 GLN A 443 SITE 4 AC3 17 PHE A 446 ZN A 501 MG A 502 HOH A 639 SITE 5 AC3 17 HOH A 666 SITE 1 AC4 8 THR A 208 PHE A 209 ASN A 325 LEU A 326 SITE 2 AC4 8 THR A 327 GLN A 330 EDO A 520 HOH A 621 SITE 1 AC5 6 THR A 215 HIS A 319 CYS A 320 ASP A 321 SITE 2 AC5 6 MET A 324 HOH A 674 SITE 1 AC6 4 HIS A 226 EDO A 507 HOH A 605 HOH A 608 SITE 1 AC7 4 HIS A 226 LYS A 313 EDO A 506 HOH A 605 SITE 1 AC8 2 SER A 251 ASP A 256 SITE 1 AC9 5 LEU A 249 THR A 252 TRP A 458 ASP A 465 SITE 2 AC9 5 ILE A 469 SITE 1 AD1 3 ALA A 167 GLU A 171 HOH A 619 SITE 1 AD2 3 SER A 429 PRO A 430 MET A 431 SITE 1 AD3 2 ARG A 477 ASN A 478 SITE 1 AD4 2 PRO A 253 ASP A 465 SITE 1 AD5 1 LYS A 168 SITE 1 AD6 3 ARG A 331 ARG A 335 HOH A 613 SITE 1 AD7 3 ASN A 174 GLU A 202 SER A 251 SITE 1 AD8 4 SER A 282 PRO A 430 CYS A 432 HOH A 620 SITE 1 AD9 4 LEU A 255 ALA A 257 VAL A 258 PHE A 259 SITE 1 AE1 7 ARG A 203 ASP A 204 LEU A 205 THR A 208 SITE 2 AE1 7 ASP A 261 ILE A 264 HOH A 601 SITE 1 AE2 4 THR A 208 ASP A 261 GLN A 330 EDO A 504 CRYST1 53.839 53.839 229.850 90.00 90.00 90.00 P 43 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 0.018574 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004351 0.00000