HEADER HYDROLASE 10-MAR-23 8OEG TITLE PDE4B BOUND TO MAPI COMPOUND 92A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DPDE4,PDE32; COMPND 5 EC: 3.1.4.53; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDE4B, DPDE4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS HUMAN PHOSPHODIESTERASE 4B, MAPI COMPOUND, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.RIZZI,E.ARMANI REVDAT 3 08-NOV-23 8OEG 1 JRNL REVDAT 2 01-NOV-23 8OEG 1 JRNL REVDAT 1 26-APR-23 8OEG 0 JRNL AUTH A.RIZZI,G.AMARI,F.PIVETTI,M.DELCANALE,F.AMADEI,A.PAPPANI, JRNL AUTH 2 L.FORNASARI,G.VILLETTI,G.MARCHINI,A.R.PISANO,V.PITOZZI, JRNL AUTH 3 M.G.PITTELLI,M.TREVISANI,M.SALVADORI,V.CENACCHI,A.FIONI, JRNL AUTH 4 P.PUCCINI,M.CIVELLI,R.PATACCHINI,C.BAKER-GLENN, JRNL AUTH 5 H.VAN DE POEL,W.BLACKABY,K.NASH,E.ARMANI JRNL TITL OPTIMIZATION OF M 3 ANTAGONIST-PDE4 INHIBITOR (MAPI) DUAL JRNL TITL 2 PHARMACOLOGY MOLECULES FOR THE TREATMENT OF COPD. JRNL REF J.MED.CHEM. V. 66 11476 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 37561958 JRNL DOI 10.1021/ACS.JMEDCHEM.3C01012 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 83.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 34670 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1771 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2377 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2714 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.51000 REMARK 3 B12 (A**2) : -0.08000 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): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.814 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2824 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2636 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3832 ; 2.476 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6061 ; 1.301 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 6.785 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;37.200 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 492 ;16.623 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.268 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.172 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3170 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 656 ; 0.002 ; 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): 1344 ; 1.962 ; 1.962 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1342 ; 1.842 ; 1.958 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1677 ; 2.520 ; 2.924 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1678 ; 2.520 ; 2.927 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1480 ; 3.235 ; 2.387 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1481 ; 3.234 ; 2.389 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2156 ; 4.977 ; 3.430 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3401 ; 5.700 ;16.538 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3402 ; 5.700 ;16.546 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 : 1.20 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 REMARK 4 REMARK 4 8OEG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS, POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36474 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 85.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM CALCIUM ACETATE, 20% PEG 400, REMARK 280 100 MM SODIUM ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.48667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.97333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 56.97333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.48667 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 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 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 245 REMARK 465 SER A 246 REMARK 465 VAL A 247 REMARK 465 SER A 248 REMARK 465 GLU A 249 REMARK 465 MET A 250 REMARK 465 ALA A 251 REMARK 465 SER A 252 REMARK 465 ASN A 253 REMARK 465 LYS A 254 REMARK 465 PHE A 255 REMARK 465 LYS A 256 REMARK 465 ARG A 257 REMARK 465 MET A 258 REMARK 465 LEU A 259 REMARK 465 ASN A 260 REMARK 465 ARG A 261 REMARK 465 GLU A 262 REMARK 465 LEU A 263 REMARK 465 THR A 264 REMARK 465 HIS A 265 REMARK 465 LEU A 266 REMARK 465 SER A 267 REMARK 465 GLU A 268 REMARK 465 MET A 269 REMARK 465 SER A 270 REMARK 465 ARG A 271 REMARK 465 SER A 272 REMARK 465 GLY A 273 REMARK 465 ASN A 274 REMARK 465 GLN A 275 REMARK 465 VAL A 276 REMARK 465 SER A 277 REMARK 465 GLU A 278 REMARK 465 TYR A 279 REMARK 465 ILE A 280 REMARK 465 SER A 281 REMARK 465 ASN A 282 REMARK 465 THR A 283 REMARK 465 PHE A 284 REMARK 465 LEU A 285 REMARK 465 ASP A 286 REMARK 465 LYS A 287 REMARK 465 GLN A 288 REMARK 465 ASN A 289 REMARK 465 ASP A 290 REMARK 465 VAL A 291 REMARK 465 GLU A 292 REMARK 465 ILE A 293 REMARK 465 PRO A 294 REMARK 465 LYS A 295 REMARK 465 VAL A 296 REMARK 465 THR A 297 REMARK 465 ALA A 298 REMARK 465 GLU A 299 REMARK 465 GLU A 300 REMARK 465 ALA A 301 REMARK 465 PRO A 302 REMARK 465 GLN A 303 REMARK 465 PRO A 304 REMARK 465 MET A 305 REMARK 465 THR A 306 REMARK 465 GLN A 307 REMARK 465 ILE A 308 REMARK 465 SER A 309 REMARK 465 GLY A 310 REMARK 465 VAL A 311 REMARK 465 LYS A 312 REMARK 465 LYS A 313 REMARK 465 LEU A 314 REMARK 465 MET A 315 REMARK 465 HIS A 316 REMARK 465 SER A 317 REMARK 465 SER A 318 REMARK 465 SER A 319 REMARK 465 LEU A 320 REMARK 465 ASN A 321 REMARK 465 ASN A 322 REMARK 465 SER A 659 REMARK 465 HIS A 660 REMARK 465 HIS A 661 REMARK 465 HIS A 662 REMARK 465 HIS A 663 REMARK 465 HIS A 664 REMARK 465 HIS A 665 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 GLY A 329 N GLY A 329 CA 0.103 REMARK 500 GLY A 329 CA GLY A 329 C 0.104 REMARK 500 SER A 401 CB SER A 401 OG -0.080 REMARK 500 SER A 524 CB SER A 524 OG -0.118 REMARK 500 ARG A 576 CD ARG A 576 NE -0.109 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 GLY A 329 C - N - CA ANGL. DEV. = -20.4 DEGREES REMARK 500 MET A 393 CG - SD - CE ANGL. DEV. = -10.7 DEGREES REMARK 500 ASP A 402 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 GLU A 435 OE1 - CD - OE2 ANGL. DEV. = -8.4 DEGREES REMARK 500 GLU A 489 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 493 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 507 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 576 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 576 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 581 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 591 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 596 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 605 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP A 605 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ASP A 643 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES 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 THR A 332 -40.27 -136.52 REMARK 500 GLU A 333 -32.73 45.82 REMARK 500 ASN A 334 52.05 -90.62 REMARK 500 ARG A 362 64.00 -118.55 REMARK 500 SER A 473 60.33 31.48 REMARK 500 ILE A 622 -57.91 -126.91 REMARK 500 GLN A 635 127.65 -35.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 329 VAL A 330 -126.93 REMARK 500 THR A 332 GLU A 333 -137.36 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 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 410 NE2 REMARK 620 2 HIS A 446 NE2 102.9 REMARK 620 3 ASP A 447 OD2 90.0 85.4 REMARK 620 4 ASP A 564 OD1 94.0 93.8 176.1 REMARK 620 5 HOH A 817 O 154.0 102.8 88.5 88.0 REMARK 620 6 HOH A 880 O 90.5 166.4 96.5 83.4 63.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 447 OD1 REMARK 620 2 HOH A 809 O 81.7 REMARK 620 3 HOH A 817 O 92.6 96.8 REMARK 620 4 HOH A 828 O 163.2 82.8 95.7 REMARK 620 5 HOH A 868 O 89.1 93.2 169.9 85.3 REMARK 620 6 HOH A 894 O 101.4 175.7 80.1 94.4 89.8 REMARK 620 N 1 2 3 4 5 DBREF 8OEG A 246 659 UNP Q07343 PDE4B_HUMAN 241 659 SEQADV 8OEG MET A 245 UNP Q07343 INITIATING METHIONINE SEQADV 8OEG LYS A 295 UNP Q07343 SER 290 CONFLICT SEQADV 8OEG VAL A 296 UNP Q07343 PRO 291 CONFLICT SEQADV 8OEG ALA A 298 UNP Q07343 GLN 293 CONFLICT SEQADV 8OEG GLU A 299 UNP Q07343 LYS 294 CONFLICT SEQADV 8OEG GLU A 300 UNP Q07343 ASP 295 CONFLICT SEQADV 8OEG A UNP Q07343 ARG 296 DELETION SEQADV 8OEG A UNP Q07343 GLU 297 DELETION SEQADV 8OEG A UNP Q07343 LYS 298 DELETION SEQADV 8OEG A UNP Q07343 LYS 299 DELETION SEQADV 8OEG A UNP Q07343 LYS 300 DELETION SEQADV 8OEG ALA A 301 UNP Q07343 LYS 301 CONFLICT SEQADV 8OEG PRO A 302 UNP Q07343 GLN 302 CONFLICT SEQADV 8OEG PRO A 304 UNP Q07343 LEU 304 CONFLICT SEQADV 8OEG HIS A 660 UNP Q07343 EXPRESSION TAG SEQADV 8OEG HIS A 661 UNP Q07343 EXPRESSION TAG SEQADV 8OEG HIS A 662 UNP Q07343 EXPRESSION TAG SEQADV 8OEG HIS A 663 UNP Q07343 EXPRESSION TAG SEQADV 8OEG HIS A 664 UNP Q07343 EXPRESSION TAG SEQADV 8OEG HIS A 665 UNP Q07343 EXPRESSION TAG SEQRES 1 A 421 MET SER VAL SER GLU MET ALA SER ASN LYS PHE LYS ARG SEQRES 2 A 421 MET LEU ASN ARG GLU LEU THR HIS LEU SER GLU MET SER SEQRES 3 A 421 ARG SER GLY ASN GLN VAL SER GLU TYR ILE SER ASN THR SEQRES 4 A 421 PHE LEU ASP LYS GLN ASN ASP VAL GLU ILE PRO LYS VAL SEQRES 5 A 421 THR ALA GLU GLU ALA PRO GLN PRO MET THR GLN ILE SER SEQRES 6 A 421 GLY VAL LYS LYS LEU MET HIS SER SER SER LEU ASN ASN SEQRES 7 A 421 THR SER ILE SER ARG PHE GLY VAL ASN THR GLU ASN GLU SEQRES 8 A 421 ASP HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN LYS TRP SEQRES 9 A 421 GLY LEU ASN ILE PHE ASN VAL ALA GLY TYR SER HIS ASN SEQRES 10 A 421 ARG PRO LEU THR CYS ILE MET TYR ALA ILE PHE GLN GLU SEQRES 11 A 421 ARG ASP LEU LEU LYS THR PHE ARG ILE SER SER ASP THR SEQRES 12 A 421 PHE ILE THR TYR MET MET THR LEU GLU ASP HIS TYR HIS SEQRES 13 A 421 SER ASP VAL ALA TYR HIS ASN SER LEU HIS ALA ALA ASP SEQRES 14 A 421 VAL ALA GLN SER THR HIS VAL LEU LEU SER THR PRO ALA SEQRES 15 A 421 LEU ASP ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA SEQRES 16 A 421 ILE PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS PRO GLY SEQRES 17 A 421 VAL SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU SEQRES 18 A 421 ALA LEU MET TYR ASN ASP GLU SER VAL LEU GLU ASN HIS SEQRES 19 A 421 HIS LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU HIS SEQRES 20 A 421 CYS ASP ILE PHE MET ASN LEU THR LYS LYS GLN ARG GLN SEQRES 21 A 421 THR LEU ARG LYS MET VAL ILE ASP MET VAL LEU ALA THR SEQRES 22 A 421 ASP MET SER LYS HIS MET SER LEU LEU ALA ASP LEU LYS SEQRES 23 A 421 THR MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL SEQRES 24 A 421 LEU LEU LEU ASP ASN TYR THR ASP ARG ILE GLN VAL LEU SEQRES 25 A 421 ARG ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR SEQRES 26 A 421 LYS SER LEU GLU LEU TYR ARG GLN TRP THR ASP ARG ILE SEQRES 27 A 421 MET GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU ARG GLU SEQRES 28 A 421 ARG GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS THR SEQRES 29 A 421 ALA SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR SEQRES 30 A 421 ILE VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL SEQRES 31 A 421 GLN PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP SEQRES 32 A 421 ASN ARG ASN TRP TYR GLN SER MET ILE PRO GLN SER HIS SEQRES 33 A 421 HIS HIS HIS HIS HIS HET ZN A 701 1 HET MG A 702 1 HET VL9 A 703 49 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM VL9 [(1~{S})-2-[3,5-BIS(CHLORANYL)-1-OXIDANYL-PYRIDIN-4- HETNAM 2 VL9 YL]-1-(3,4-DIMETHOXYPHENYL)ETHYL] 5-[[[(1~{R})-2- HETNAM 3 VL9 [[(3~{R})-1-AZABICYCLO[2.2.2]OCTAN-3-YL]OXY]-2- HETNAM 4 VL9 OXIDANYLIDENE-1-PHENYL-ETHYL]AMINO]METHYL]THIOPHENE-2- HETNAM 5 VL9 CARBOXYLATE FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 VL9 C36 H38 CL2 N3 O7 S FORMUL 5 HOH *116(H2 O) HELIX 1 AA1 THR A 323 PHE A 328 1 6 HELIX 2 AA2 ASN A 334 GLU A 343 1 10 HELIX 3 AA3 ASN A 351 SER A 359 1 9 HELIX 4 AA4 ARG A 362 ARG A 375 1 14 HELIX 5 AA5 ASP A 376 PHE A 381 1 6 HELIX 6 AA6 SER A 384 HIS A 398 1 15 HELIX 7 AA7 ASN A 407 SER A 423 1 17 HELIX 8 AA8 THR A 424 ASP A 428 5 5 HELIX 9 AA9 THR A 432 HIS A 446 1 15 HELIX 10 AB1 SER A 454 THR A 461 1 8 HELIX 11 AB2 SER A 463 ASN A 470 1 8 HELIX 12 AB3 SER A 473 LEU A 486 1 14 HELIX 13 AB4 LEU A 487 GLU A 489 5 3 HELIX 14 AB5 THR A 499 ALA A 516 1 18 HELIX 15 AB6 THR A 517 SER A 520 5 4 HELIX 16 AB7 LYS A 521 THR A 535 1 15 HELIX 17 AB8 ASN A 548 LEU A 565 1 18 HELIX 18 AB9 SER A 566 LYS A 570 5 5 HELIX 19 AC1 SER A 571 ARG A 596 1 26 HELIX 20 AC2 SER A 610 ILE A 622 1 13 HELIX 21 AC3 ILE A 622 VAL A 634 1 13 HELIX 22 AC4 ALA A 638 MET A 655 1 18 LINK NE2 HIS A 410 ZN ZN A 701 1555 1555 2.11 LINK NE2 HIS A 446 ZN ZN A 701 1555 1555 2.14 LINK OD2 ASP A 447 ZN ZN A 701 1555 1555 2.11 LINK OD1 ASP A 447 MG MG A 702 1555 1555 2.17 LINK OD1 ASP A 564 ZN ZN A 701 1555 1555 2.10 LINK ZN ZN A 701 O HOH A 817 1555 1555 2.39 LINK ZN ZN A 701 O HOH A 880 1555 1555 2.40 LINK MG MG A 702 O HOH A 809 1555 1555 2.27 LINK MG MG A 702 O HOH A 817 1555 1555 2.27 LINK MG MG A 702 O HOH A 828 1555 1555 2.24 LINK MG MG A 702 O HOH A 868 1555 1555 2.26 LINK MG MG A 702 O HOH A 894 1555 1555 2.25 CISPEP 1 GLN A 635 PRO A 636 0 -2.39 CRYST1 95.760 95.760 85.460 90.00 90.00 120.00 P 31 2 1 6 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 0.010443 0.006029 0.000000 0.00000 SCALE2 0.000000 0.012058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011701 0.00000