HEADER HYDROLASE 29-NOV-21 7W4X TITLE CRYSTAL STRUCTURE OF PDE4D CATALYTIC DOMAIN COMPLEXED WITH 17 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPDE3,PDE43; 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: PDE4D, DPDE3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS CAMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE 4D, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.HUANG,H.-B.LUO REVDAT 3 29-NOV-23 7W4X 1 REMARK REVDAT 2 23-MAR-22 7W4X 1 JRNL REVDAT 1 16-MAR-22 7W4X 0 JRNL AUTH Z.SONG,Y.Y.HUANG,K.Q.HOU,L.LIU,F.ZHOU,Y.HUANG,G.WAN,H.B.LUO, JRNL AUTH 2 X.F.XIONG JRNL TITL DISCOVERY AND STRUCTURAL OPTIMIZATION OF TODDACOUMALONE JRNL TITL 2 DERIVATIVES AS NOVEL PDE4 INHIBITORS FOR THE TOPICAL JRNL TITL 3 TREATMENT OF PSORIASIS. JRNL REF J.MED.CHEM. V. 65 4238 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35188767 JRNL DOI 10.1021/ACS.JMEDCHEM.1C02058 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 39228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.795 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.6300 - 5.1542 0.98 3001 167 0.2075 0.2391 REMARK 3 2 5.1542 - 4.0990 0.99 2917 146 0.2017 0.2324 REMARK 3 3 4.0990 - 3.5832 1.00 2898 159 0.2160 0.2243 REMARK 3 4 3.5832 - 3.2566 1.00 2902 138 0.2272 0.2733 REMARK 3 5 3.2566 - 3.0238 1.00 2869 130 0.2375 0.2545 REMARK 3 6 3.0238 - 2.8459 1.00 2854 149 0.2397 0.2489 REMARK 3 7 2.8459 - 2.7036 1.00 2873 149 0.2419 0.2620 REMARK 3 8 2.7036 - 2.5861 1.00 2833 166 0.2505 0.2606 REMARK 3 9 2.5861 - 2.4866 1.00 2855 140 0.2584 0.3112 REMARK 3 10 2.4866 - 2.4009 1.00 2833 130 0.2480 0.2638 REMARK 3 11 2.4009 - 2.3259 1.00 2846 150 0.2487 0.2874 REMARK 3 12 2.3259 - 2.2595 1.00 2881 117 0.2585 0.2499 REMARK 3 13 2.2595 - 2.2001 1.00 2785 140 0.2644 0.3000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.232 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 5404 REMARK 3 ANGLE : 0.596 7350 REMARK 3 CHIRALITY : 0.041 842 REMARK 3 PLANARITY : 0.005 976 REMARK 3 DIHEDRAL : 21.436 2010 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7W4X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300025991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 171.39.46 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39230 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 22.634 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 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: 5WQA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.4), 0.1 M MGCL2, 15% REMARK 280 PEG 3350, 10% ISOPROPANOL, AND 25% ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 28.90500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.64400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.15050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.64400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.15050 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 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 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 TOTAL BURIED SURFACE AREA: 80 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL 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 78 REMARK 465 ILE A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 PHE A 82 REMARK 465 GLY A 83 REMARK 465 VAL A 84 REMARK 465 LYS A 85 REMARK 465 THR A 86 REMARK 465 GLU A 87 REMARK 465 GLN A 412 REMARK 465 SER A 413 REMARK 465 PRO A 414 REMARK 465 SER A 415 REMARK 465 PRO A 416 REMARK 465 ALA A 417 REMARK 465 PRO A 418 REMARK 465 ASP A 419 REMARK 465 ASP A 420 REMARK 465 PRO A 421 REMARK 465 GLU A 422 REMARK 465 GLU A 423 REMARK 465 GLY A 424 REMARK 465 ARG A 425 REMARK 465 GLN A 426 REMARK 465 GLY A 427 REMARK 465 GLN A 428 REMARK 465 THR A 429 REMARK 465 GLU A 430 REMARK 465 LYS A 431 REMARK 465 PHE A 432 REMARK 465 GLN A 433 REMARK 465 PHE A 434 REMARK 465 GLU A 435 REMARK 465 LEU A 436 REMARK 465 THR A 437 REMARK 465 LEU A 438 REMARK 465 GLU A 439 REMARK 465 GLU A 440 REMARK 465 ASP A 441 REMARK 465 GLY A 442 REMARK 465 GLU A 443 REMARK 465 SER A 444 REMARK 465 ASP A 445 REMARK 465 THR A 446 REMARK 465 GLU A 447 REMARK 465 LYS A 448 REMARK 465 ASP A 449 REMARK 465 ALA A 450 REMARK 465 SER B 78 REMARK 465 ILE B 79 REMARK 465 PRO B 80 REMARK 465 ARG B 81 REMARK 465 PHE B 82 REMARK 465 GLY B 83 REMARK 465 VAL B 84 REMARK 465 LYS B 85 REMARK 465 THR B 86 REMARK 465 GLU B 87 REMARK 465 GLN B 412 REMARK 465 SER B 413 REMARK 465 PRO B 414 REMARK 465 SER B 415 REMARK 465 PRO B 416 REMARK 465 ALA B 417 REMARK 465 PRO B 418 REMARK 465 ASP B 419 REMARK 465 ASP B 420 REMARK 465 PRO B 421 REMARK 465 GLU B 422 REMARK 465 GLU B 423 REMARK 465 GLY B 424 REMARK 465 ARG B 425 REMARK 465 GLN B 426 REMARK 465 GLY B 427 REMARK 465 GLN B 428 REMARK 465 THR B 429 REMARK 465 GLU B 430 REMARK 465 LYS B 431 REMARK 465 PHE B 432 REMARK 465 GLN B 433 REMARK 465 PHE B 434 REMARK 465 GLU B 435 REMARK 465 LEU B 436 REMARK 465 THR B 437 REMARK 465 LEU B 438 REMARK 465 GLU B 439 REMARK 465 GLU B 440 REMARK 465 ASP B 441 REMARK 465 GLY B 442 REMARK 465 GLU B 443 REMARK 465 SER B 444 REMARK 465 ASP B 445 REMARK 465 THR B 446 REMARK 465 GLU B 447 REMARK 465 LYS B 448 REMARK 465 ASP B 449 REMARK 465 ALA B 450 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 612 O HOH A 707 1.84 REMARK 500 O HOH A 649 O HOH A 724 1.84 REMARK 500 O LYS B 101 O HOH B 601 1.88 REMARK 500 OD1 ASP B 397 O HOH B 602 1.91 REMARK 500 O HOH B 626 O HOH B 642 1.91 REMARK 500 OE1 GLU A 288 O HOH A 601 1.97 REMARK 500 O HOH B 686 O HOH B 703 1.97 REMARK 500 O ASP A 130 O HOH A 602 1.98 REMARK 500 NE2 GLN A 407 O HOH A 603 1.98 REMARK 500 O HOH A 642 O HOH A 755 2.02 REMARK 500 OE1 GLN A 393 O HOH A 604 2.04 REMARK 500 O HOH B 682 O HOH B 700 2.06 REMARK 500 N THR A 134 O HOH A 602 2.07 REMARK 500 O HOH A 725 O HOH A 732 2.09 REMARK 500 O HOH A 668 O HOH A 743 2.10 REMARK 500 O ASP B 391 O HOH B 603 2.12 REMARK 500 OE2 GLU A 128 O HOH A 605 2.12 REMARK 500 O HOH A 694 O HOH A 719 2.13 REMARK 500 NE2 GLN A 127 O HOH A 606 2.13 REMARK 500 O THR A 178 O HOH A 607 2.15 REMARK 500 O ASP A 151 O HOH A 608 2.16 REMARK 500 NZ LYS A 133 O HOH A 609 2.16 REMARK 500 O HOH A 608 O HOH A 723 2.17 REMARK 500 O PRO B 411 O HOH B 604 2.17 REMARK 500 O HOH A 654 O HOH A 747 2.18 REMARK 500 O HOH B 684 O HOH B 699 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 O HOH A 744 O HOH B 615 3644 2.08 REMARK 500 OD1 ASP B 301 O HOH A 608 3654 2.16 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 GLU B 182 CD GLU B 182 OE2 -0.069 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 161 -167.55 -119.03 REMARK 500 LEU A 319 40.72 -103.52 REMARK 500 ILE A 376 -62.40 -130.40 REMARK 500 GLU B 89 41.13 -85.58 REMARK 500 ALA B 183 -52.54 62.12 REMARK 500 VAL B 184 -48.36 -3.16 REMARK 500 THR B 289 36.44 -97.13 REMARK 500 THR B 293 -111.56 155.96 REMARK 500 SER B 294 -70.49 50.68 REMARK 500 LEU B 319 40.30 -102.71 REMARK 500 ASN B 362 27.56 -154.13 REMARK 500 ILE B 376 -61.35 -128.26 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 164 NE2 REMARK 620 2 HIS A 200 NE2 90.2 REMARK 620 3 ASP A 201 OD2 87.6 79.1 REMARK 620 4 ASP A 318 OD1 83.1 91.5 166.8 REMARK 620 5 HOH A 626 O 172.0 96.2 88.8 101.6 REMARK 620 N 1 2 3 4 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 201 OD1 REMARK 620 2 HOH A 625 O 85.5 REMARK 620 3 HOH A 626 O 97.6 103.4 REMARK 620 4 HOH A 631 O 166.6 86.1 94.5 REMARK 620 5 HOH A 683 O 90.2 89.9 165.0 79.3 REMARK 620 6 HOH A 692 O 94.6 170.9 85.6 92.0 81.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 88.4 REMARK 620 3 ASP B 201 OD2 89.7 82.3 REMARK 620 4 ASP B 318 OD1 84.2 89.0 169.5 REMARK 620 5 8G7 B 503 O2 90.1 170.1 107.5 81.1 REMARK 620 6 HOH B 650 O 173.8 97.8 91.0 96.0 83.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 621 O 81.0 REMARK 620 3 HOH B 625 O 158.7 80.0 REMARK 620 4 HOH B 649 O 103.6 172.5 94.3 REMARK 620 5 HOH B 650 O 103.7 89.5 85.7 95.0 REMARK 620 6 HOH B 660 O 88.0 91.0 82.7 83.4 168.2 REMARK 620 N 1 2 3 4 5 DBREF 7W4X A 78 449 UNP Q08499 PDE4D_HUMAN 380 751 DBREF 7W4X B 78 449 UNP Q08499 PDE4D_HUMAN 380 751 SEQADV 7W4X ALA A 450 UNP Q08499 EXPRESSION TAG SEQADV 7W4X ALA B 450 UNP Q08499 EXPRESSION TAG SEQRES 1 A 373 SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP SEQRES 2 A 373 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 3 A 373 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 4 A 373 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 5 A 373 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 6 A 373 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 7 A 373 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 8 A 373 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 A 373 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 A 373 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 A 373 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 A 373 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 13 A 373 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 14 A 373 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 15 A 373 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 16 A 373 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 17 A 373 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 A 373 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 19 A 373 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 A 373 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 A 373 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 22 A 373 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 23 A 373 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 A 373 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 25 A 373 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 A 373 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER PRO SER SEQRES 27 A 373 PRO ALA PRO ASP ASP PRO GLU GLU GLY ARG GLN GLY GLN SEQRES 28 A 373 THR GLU LYS PHE GLN PHE GLU LEU THR LEU GLU GLU ASP SEQRES 29 A 373 GLY GLU SER ASP THR GLU LYS ASP ALA SEQRES 1 B 373 SER ILE PRO ARG PHE GLY VAL LYS THR GLU GLN GLU ASP SEQRES 2 B 373 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 3 B 373 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 4 B 373 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 5 B 373 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 6 B 373 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 7 B 373 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 8 B 373 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 B 373 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 B 373 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 B 373 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 B 373 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 13 B 373 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 14 B 373 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 15 B 373 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 16 B 373 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 17 B 373 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 B 373 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 19 B 373 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 B 373 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 B 373 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 22 B 373 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 23 B 373 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 B 373 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 25 B 373 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 B 373 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER PRO SER SEQRES 27 B 373 PRO ALA PRO ASP ASP PRO GLU GLU GLY ARG GLN GLY GLN SEQRES 28 B 373 THR GLU LYS PHE GLN PHE GLU LEU THR LEU GLU GLU ASP SEQRES 29 B 373 GLY GLU SER ASP THR GLU LYS ASP ALA HET ZN A 501 1 HET MG A 502 1 HET 8G7 A 503 24 HET ZN B 501 1 HET MG B 502 1 HET 8G7 B 503 24 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 8G7 (2R,4S)-2-(2-HYDROXYETHYL)-2,6-DIMETHYL-4-(2- HETNAM 2 8G7 METHYLPROP-1-ENYL)-3,4-DIHYDROPYRANO[3,2-C][1, HETNAM 3 8G7 8]NAPHTHYRIDIN-5-ONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 8G7 2(C19 H24 N2 O3) FORMUL 9 HOH *262(H2 O) HELIX 1 AA1 GLN A 88 LEU A 96 1 9 HELIX 2 AA2 GLU A 97 VAL A 99 5 3 HELIX 3 AA3 HIS A 105 SER A 113 1 9 HELIX 4 AA4 ARG A 116 ARG A 129 1 14 HELIX 5 AA5 ASP A 130 PHE A 135 1 6 HELIX 6 AA6 PRO A 138 HIS A 152 1 15 HELIX 7 AA7 ASN A 161 SER A 177 1 17 HELIX 8 AA8 THR A 178 GLU A 182 5 5 HELIX 9 AA9 THR A 186 HIS A 200 1 15 HELIX 10 AB1 SER A 208 THR A 215 1 8 HELIX 11 AB2 SER A 217 ASN A 224 1 8 HELIX 12 AB3 SER A 227 LEU A 240 1 14 HELIX 13 AB4 LEU A 241 GLU A 243 5 3 HELIX 14 AB5 THR A 253 ALA A 270 1 18 HELIX 15 AB6 THR A 271 SER A 274 5 4 HELIX 16 AB7 LYS A 275 THR A 289 1 15 HELIX 17 AB8 ASN A 302 LEU A 319 1 18 HELIX 18 AB9 SER A 320 LYS A 324 5 5 HELIX 19 AC1 PRO A 325 ARG A 350 1 26 HELIX 20 AC2 SER A 364 ILE A 376 1 13 HELIX 21 AC3 ILE A 376 VAL A 388 1 13 HELIX 22 AC4 ALA A 392 THR A 409 1 18 HELIX 23 AC5 ASP B 90 GLU B 97 1 8 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ARG B 129 1 14 HELIX 26 AC8 ASP B 130 PHE B 135 1 6 HELIX 27 AC9 PRO B 138 HIS B 152 1 15 HELIX 28 AD1 ASN B 161 LEU B 176 1 16 HELIX 29 AD2 SER B 177 GLU B 182 5 6 HELIX 30 AD3 THR B 186 HIS B 200 1 15 HELIX 31 AD4 SER B 208 THR B 215 1 8 HELIX 32 AD5 SER B 217 ASN B 224 1 8 HELIX 33 AD6 SER B 227 LEU B 240 1 14 HELIX 34 AD7 LEU B 241 GLU B 243 5 3 HELIX 35 AD8 THR B 253 ALA B 270 1 18 HELIX 36 AD9 THR B 271 SER B 274 5 4 HELIX 37 AE1 LYS B 275 THR B 289 1 15 HELIX 38 AE2 ASN B 302 LEU B 319 1 18 HELIX 39 AE3 SER B 320 LYS B 324 5 5 HELIX 40 AE4 PRO B 325 GLY B 351 1 27 HELIX 41 AE5 SER B 364 ILE B 376 1 13 HELIX 42 AE6 ILE B 376 VAL B 388 1 13 HELIX 43 AE7 ALA B 392 THR B 409 1 18 LINK NE2 HIS A 164 ZN ZN A 501 1555 1555 2.32 LINK NE2 HIS A 200 ZN ZN A 501 1555 1555 2.30 LINK OD2 ASP A 201 ZN ZN A 501 1555 1555 2.15 LINK OD1 ASP A 201 MG MG A 502 1555 1555 2.17 LINK OD1 ASP A 318 ZN ZN A 501 1555 1555 2.18 LINK ZN ZN A 501 O HOH A 626 1555 1555 2.08 LINK MG MG A 502 O HOH A 625 1555 1555 2.15 LINK MG MG A 502 O HOH A 626 1555 1555 1.99 LINK MG MG A 502 O HOH A 631 1555 1555 2.25 LINK MG MG A 502 O HOH A 683 1555 1555 2.18 LINK MG MG A 502 O HOH A 692 1555 1555 2.17 LINK NE2 HIS B 164 ZN ZN B 501 1555 1555 2.26 LINK NE2 HIS B 200 ZN ZN B 501 1555 1555 2.37 LINK OD2 ASP B 201 ZN ZN B 501 1555 1555 2.10 LINK OD1 ASP B 201 MG MG B 502 1555 1555 2.09 LINK OD1 ASP B 318 ZN ZN B 501 1555 1555 2.27 LINK ZN ZN B 501 O2 8G7 B 503 1555 1555 2.58 LINK ZN ZN B 501 O HOH B 650 1555 1555 2.28 LINK MG MG B 502 O HOH B 621 1555 1555 1.84 LINK MG MG B 502 O HOH B 625 1555 1555 2.42 LINK MG MG B 502 O HOH B 649 1555 1555 2.12 LINK MG MG B 502 O HOH B 650 1555 1555 1.94 LINK MG MG B 502 O HOH B 660 1555 1555 2.35 CISPEP 1 HIS A 389 PRO A 390 0 1.09 CISPEP 2 HIS B 389 PRO B 390 0 -2.74 CRYST1 57.810 80.301 163.288 90.00 90.00 90.00 P 21 21 21 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 0.017298 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006124 0.00000