PDB Short entry for 3K4S HEADER HYDROLASE 06-OCT-09 3K4S TITLE THE STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN PDE4D WITH 4-(3-BUTOXY- TITLE 2 4-METHOXYPHENYL)METHYL-2-IMIDAZOLIDONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 388-654; 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, DPDE3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ARCTIC EXPRESS RP (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NUCLEOTIDE BINDING, PHOSPHODIESTERASE, ALTERNATIVE SPLICING, CAMP, KEYWDS 2 CYTOPLASM, CYTOSKELETON, HYDROLASE, MEMBRANE, METAL-BINDING, KEYWDS 3 PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.CRAWLEY,R.K.Y.CHENG,M.WOOD,J.BARKER,B.FELICETTI,M.WHITTAKER REVDAT 2 06-SEP-23 3K4S 1 REMARK LINK REVDAT 1 20-OCT-09 3K4S 0 JRNL AUTH L.CRAWLEY,R.K.Y.CHENG,M.WOOD,J.BARKER,B.FELICETTI, JRNL AUTH 2 M.WHITTAKER JRNL TITL THE STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN PDE4D WITH JRNL TITL 2 4-(3-BUTOXY-4-METHOXYPHENYL)METHYL-2-IMIDAZOLIDONE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31860 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1699 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2348 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2665 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.57000 REMARK 3 B22 (A**2) : 1.57000 REMARK 3 B33 (A**2) : -3.15000 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): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.034 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2773 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3774 ; 1.608 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 338 ; 5.331 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;36.447 ;25.177 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 490 ;15.685 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.781 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 432 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2097 ; 0.008 ; 0.021 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): 1664 ; 0.945 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2715 ; 1.746 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1109 ; 2.897 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1055 ; 4.635 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 3K4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR. KIRKPATRICK BAEZ REMARK 200 BIMORPH MIRROR PAIR FOR REMARK 200 HORIZONTAL AND VERTICAL FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33561 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 46.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.490 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.08 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1Y2B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M AMMONIUM SULPHATE, 0.1M SODIUM REMARK 280 CITRATE PH 5.6, 1.0M LITHIUM SULPHATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 74.38300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.19150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 111.57450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.38300 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 111.57450 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 37.19150 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.38300 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 65 REMARK 465 GLY A 66 REMARK 465 SER A 67 REMARK 465 SER A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 SER A 75 REMARK 465 SER A 76 REMARK 465 GLY A 77 REMARK 465 LEU A 78 REMARK 465 VAL A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 GLY A 82 REMARK 465 SER A 83 REMARK 465 SER A 413 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 254 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 548 O HOH A 619 2.02 REMARK 500 O HOH A 25 O HOH A 606 2.10 REMARK 500 OE1 GLU A 97 O HOH A 576 2.18 REMARK 500 NH1 ARG A 108 O HOH A 482 2.18 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 OG SER A 408 O HOH A 609 4554 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 254 CB LYS A 254 CG -0.234 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 104 132.36 -39.56 REMARK 500 ALA A 183 8.30 58.07 REMARK 500 ASN A 362 58.28 -153.89 REMARK 500 ILE A 376 -58.17 -121.29 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 164 NE2 REMARK 620 2 HIS A 200 NE2 92.6 REMARK 620 3 ASP A 201 OD2 89.3 81.3 REMARK 620 4 ASP A 318 OD1 88.9 89.4 170.5 REMARK 620 5 HOH A 547 O 168.2 97.9 97.6 85.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 415 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 201 OD1 REMARK 620 2 HOH A 539 O 86.9 REMARK 620 3 HOH A 540 O 96.1 93.2 REMARK 620 4 HOH A 547 O 110.9 161.3 90.5 REMARK 620 5 HOH A 548 O 92.4 76.9 166.7 96.1 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0MO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 415 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IAK RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH DIFFERENT LIGAND. DBREF 3K4S A 86 413 UNP Q08499 PDE4D_HUMAN 388 715 SEQADV 3K4S MET A 65 UNP Q08499 EXPRESSION TAG SEQADV 3K4S GLY A 66 UNP Q08499 EXPRESSION TAG SEQADV 3K4S SER A 67 UNP Q08499 EXPRESSION TAG SEQADV 3K4S SER A 68 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 69 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 70 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 71 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 72 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 73 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 74 UNP Q08499 EXPRESSION TAG SEQADV 3K4S SER A 75 UNP Q08499 EXPRESSION TAG SEQADV 3K4S SER A 76 UNP Q08499 EXPRESSION TAG SEQADV 3K4S GLY A 77 UNP Q08499 EXPRESSION TAG SEQADV 3K4S LEU A 78 UNP Q08499 EXPRESSION TAG SEQADV 3K4S VAL A 79 UNP Q08499 EXPRESSION TAG SEQADV 3K4S PRO A 80 UNP Q08499 EXPRESSION TAG SEQADV 3K4S ARG A 81 UNP Q08499 EXPRESSION TAG SEQADV 3K4S GLY A 82 UNP Q08499 EXPRESSION TAG SEQADV 3K4S SER A 83 UNP Q08499 EXPRESSION TAG SEQADV 3K4S HIS A 84 UNP Q08499 EXPRESSION TAG SEQADV 3K4S MET A 85 UNP Q08499 EXPRESSION TAG SEQRES 1 A 349 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 349 LEU VAL PRO ARG GLY SER HIS MET THR GLU GLN GLU ASP SEQRES 3 A 349 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 4 A 349 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 5 A 349 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 6 A 349 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 7 A 349 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 8 A 349 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 9 A 349 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 10 A 349 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 11 A 349 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 12 A 349 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 13 A 349 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 14 A 349 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 15 A 349 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 16 A 349 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 17 A 349 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 18 A 349 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 19 A 349 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 20 A 349 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 21 A 349 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 22 A 349 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 23 A 349 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 24 A 349 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 25 A 349 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 26 A 349 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 27 A 349 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER HET ZN A 1 1 HET 0MO A 414 20 HET MG A 415 1 HETNAM ZN ZINC ION HETNAM 0MO (4R)-4-(3-BUTOXY-4-METHOXYBENZYL)IMIDAZOLIDIN-2-ONE HETNAM MG MAGNESIUM ION HETSYN 0MO 4-(3-BUTOXY-4-METHOXYPHENYL)METHYL-2-IMIDAZOLIDONE FORMUL 2 ZN ZN 2+ FORMUL 3 0MO C15 H22 N2 O3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *268(H2 O) HELIX 1 1 ASP A 90 GLU A 97 1 8 HELIX 2 2 HIS A 105 SER A 113 1 9 HELIX 3 3 ARG A 116 ARG A 129 1 14 HELIX 4 4 ASP A 130 PHE A 135 1 6 HELIX 5 5 PRO A 138 HIS A 152 1 15 HELIX 6 6 ASN A 161 SER A 177 1 17 HELIX 7 7 THR A 178 GLU A 182 5 5 HELIX 8 8 THR A 186 HIS A 200 1 15 HELIX 9 9 SER A 208 THR A 215 1 8 HELIX 10 10 SER A 217 TYR A 223 1 7 HELIX 11 11 SER A 227 LEU A 241 1 15 HELIX 12 12 THR A 253 ALA A 270 1 18 HELIX 13 13 THR A 271 SER A 274 5 4 HELIX 14 14 LYS A 275 THR A 289 1 15 HELIX 15 15 ASN A 302 LEU A 319 1 18 HELIX 16 16 SER A 320 LYS A 324 5 5 HELIX 17 17 PRO A 325 ARG A 350 1 26 HELIX 18 18 SER A 364 ILE A 376 1 13 HELIX 19 19 ILE A 376 VAL A 388 1 13 HELIX 20 20 ALA A 392 THR A 409 1 18 LINK ZN ZN A 1 NE2 HIS A 164 1555 1555 2.33 LINK ZN ZN A 1 NE2 HIS A 200 1555 1555 2.30 LINK ZN ZN A 1 OD2 ASP A 201 1555 1555 2.10 LINK ZN ZN A 1 OD1 ASP A 318 1555 1555 2.24 LINK ZN ZN A 1 O HOH A 547 1555 1555 2.33 LINK OD1 ASP A 201 MG MG A 415 1555 1555 2.17 LINK MG MG A 415 O HOH A 539 1555 1555 2.45 LINK MG MG A 415 O HOH A 540 1555 1555 2.29 LINK MG MG A 415 O HOH A 547 1555 1555 2.18 LINK MG MG A 415 O HOH A 548 1555 1555 2.24 CISPEP 1 HIS A 389 PRO A 390 0 -0.58 SITE 1 AC1 7 HIS A 164 HIS A 200 ASP A 201 ASP A 318 SITE 2 AC1 7 MG A 415 HOH A 542 HOH A 547 SITE 1 AC2 11 TYR A 159 MET A 273 ASN A 321 THR A 333 SITE 2 AC2 11 ILE A 336 MET A 337 PHE A 340 GLN A 369 SITE 3 AC2 11 PHE A 372 HOH A 565 HOH A 619 SITE 1 AC3 8 ZN A 1 ASP A 201 HOH A 539 HOH A 540 SITE 2 AC3 8 HOH A 541 HOH A 547 HOH A 548 HOH A 619 CRYST1 83.217 83.217 148.766 90.00 90.00 90.00 P 41 2 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 0.012017 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012017 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006722 0.00000