HEADER HYDROLASE 05-DEC-18 6IWI TITLE CRYSTAL STRUCTURE OF PDE5A IN COMPLEX WITH A NOVEL INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHODIESTERASE TYPE 5, CGMP-BINDING CGMP-SPECIFIC COMPND 5 PHOSPHODIESTERASE,CGB-PDE; COMPND 6 EC: 3.1.4.35; 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: PDE5A, PDE5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PDE5A, INHIBITOR, COMPLEX STRUCTURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.L.ZHANG,Y.C.XU REVDAT 3 27-MAR-24 6IWI 1 REMARK REVDAT 2 23-DEC-20 6IWI 1 JRNL LINK REVDAT 1 11-DEC-19 6IWI 0 JRNL AUTH Z.WANG,X.JIANG,X.ZHANG,G.TIAN,R.YANG,J.WU,X.ZOU,Z.LIU, JRNL AUTH 2 X.YANG,C.WU,J.SHI,J.LI,J.SUO,Y.WANG,R.ZHANG,Z.XU,X.GONG, JRNL AUTH 3 Y.HE,W.ZHU,H.A.AISA,H.JIANG,Y.XU,J.SHEN JRNL TITL PHARMACOKINETICS-DRIVEN OPTIMIZATION OF 4(3 H)-PYRIMIDINONES JRNL TITL 2 AS PHOSPHODIESTERASE TYPE 5 INHIBITORS LEADING TO TPN171, A JRNL TITL 3 CLINICAL CANDIDATE FOR THE TREATMENT OF PULMONARY ARTERIAL JRNL TITL 4 HYPERTENSION. JRNL REF J.MED.CHEM. V. 62 4979 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31021628 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00123 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 22358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 1080 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 36.3986 - 4.3074 1.00 2981 154 0.1572 0.2047 REMARK 3 2 4.3074 - 3.4198 1.00 2837 147 0.1544 0.1665 REMARK 3 3 3.4198 - 2.9877 1.00 2826 134 0.1847 0.2268 REMARK 3 4 2.9877 - 2.7146 1.00 2829 138 0.1961 0.2576 REMARK 3 5 2.7146 - 2.5201 1.00 2768 161 0.1986 0.2488 REMARK 3 6 2.5201 - 2.3716 1.00 2748 146 0.2149 0.2731 REMARK 3 7 2.3716 - 2.2528 0.93 2604 117 0.2440 0.3391 REMARK 3 8 2.2528 - 2.1548 0.61 1685 83 0.2999 0.2988 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.40 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 : 0.002 2358 REMARK 3 ANGLE : 0.435 3195 REMARK 3 CHIRALITY : 0.034 368 REMARK 3 PLANARITY : 0.003 404 REMARK 3 DIHEDRAL : 15.748 1429 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 536 THROUGH 554 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1799 -12.2010 -13.2947 REMARK 3 T TENSOR REMARK 3 T11: 0.2446 T22: 0.2047 REMARK 3 T33: 0.1458 T12: -0.0872 REMARK 3 T13: 0.0636 T23: 0.0633 REMARK 3 L TENSOR REMARK 3 L11: 0.0005 L22: 0.0068 REMARK 3 L33: 0.0046 L12: 0.0015 REMARK 3 L13: -0.0009 L23: 0.0010 REMARK 3 S TENSOR REMARK 3 S11: 0.0040 S12: 0.0060 S13: 0.0028 REMARK 3 S21: -0.0220 S22: 0.0098 S23: -0.0059 REMARK 3 S31: -0.0130 S32: -0.0022 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 555 THROUGH 581 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.8933 -14.2879 -3.6404 REMARK 3 T TENSOR REMARK 3 T11: 0.2188 T22: 0.1128 REMARK 3 T33: 0.0969 T12: -0.1410 REMARK 3 T13: 0.0544 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.0042 L22: 0.0049 REMARK 3 L33: 0.0007 L12: 0.0049 REMARK 3 L13: -0.0003 L23: 0.0005 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: 0.0165 S13: -0.0047 REMARK 3 S21: -0.0071 S22: 0.0106 S23: -0.0254 REMARK 3 S31: -0.0149 S32: 0.0101 S33: 0.0146 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 582 THROUGH 604 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.7640 -23.6284 -11.5806 REMARK 3 T TENSOR REMARK 3 T11: 0.1808 T22: 0.1192 REMARK 3 T33: 0.0907 T12: -0.0957 REMARK 3 T13: -0.0056 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.0110 L22: 0.0149 REMARK 3 L33: 0.0028 L12: 0.0125 REMARK 3 L13: 0.0060 L23: 0.0063 REMARK 3 S TENSOR REMARK 3 S11: -0.0078 S12: 0.0317 S13: -0.0242 REMARK 3 S21: -0.0375 S22: 0.0300 S23: -0.0206 REMARK 3 S31: 0.0008 S32: -0.0139 S33: 0.0100 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 679 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1131 -22.8328 3.0105 REMARK 3 T TENSOR REMARK 3 T11: 0.1019 T22: 0.0203 REMARK 3 T33: 0.0666 T12: -0.1649 REMARK 3 T13: -0.0103 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.0164 L22: 0.0294 REMARK 3 L33: 0.0071 L12: 0.0215 REMARK 3 L13: 0.0096 L23: 0.0102 REMARK 3 S TENSOR REMARK 3 S11: 0.0307 S12: -0.0022 S13: -0.0582 REMARK 3 S21: 0.0007 S22: 0.0207 S23: -0.0322 REMARK 3 S31: 0.0163 S32: -0.0036 S33: 0.0930 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 680 THROUGH 705 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.1452 -28.7894 -2.5769 REMARK 3 T TENSOR REMARK 3 T11: 0.1571 T22: 0.1894 REMARK 3 T33: 0.1287 T12: -0.1615 REMARK 3 T13: -0.0041 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.0018 L22: 0.0087 REMARK 3 L33: 0.0032 L12: 0.0012 REMARK 3 L13: -0.0003 L23: -0.0033 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: 0.0017 S13: 0.0100 REMARK 3 S21: -0.0056 S22: 0.0047 S23: 0.0375 REMARK 3 S31: 0.0026 S32: -0.0119 S33: 0.0071 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 706 THROUGH 723 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4801 -36.2592 -0.8598 REMARK 3 T TENSOR REMARK 3 T11: 0.1681 T22: 0.0514 REMARK 3 T33: 0.0910 T12: -0.1428 REMARK 3 T13: -0.0177 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.0028 L22: 0.0047 REMARK 3 L33: 0.0004 L12: 0.0005 REMARK 3 L13: -0.0012 L23: -0.0001 REMARK 3 S TENSOR REMARK 3 S11: 0.0072 S12: 0.0016 S13: -0.0128 REMARK 3 S21: 0.0091 S22: -0.0027 S23: 0.0022 REMARK 3 S31: 0.0027 S32: 0.0014 S33: 0.0074 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 724 THROUGH 748 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.3009 -37.7443 15.2016 REMARK 3 T TENSOR REMARK 3 T11: 0.2953 T22: 0.1446 REMARK 3 T33: 0.2063 T12: -0.0525 REMARK 3 T13: -0.1137 T23: 0.0253 REMARK 3 L TENSOR REMARK 3 L11: 0.0007 L22: 0.0014 REMARK 3 L33: 0.0012 L12: -0.0014 REMARK 3 L13: -0.0006 L23: -0.0013 REMARK 3 S TENSOR REMARK 3 S11: 0.0422 S12: 0.0063 S13: -0.0244 REMARK 3 S21: 0.0239 S22: 0.0358 S23: -0.0180 REMARK 3 S31: 0.0257 S32: 0.0173 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 749 THROUGH 771 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.2562 -29.4512 9.0564 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.0505 REMARK 3 T33: 0.1163 T12: -0.0779 REMARK 3 T13: -0.0764 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.0088 L22: 0.0164 REMARK 3 L33: 0.0123 L12: -0.0041 REMARK 3 L13: -0.0096 L23: 0.0054 REMARK 3 S TENSOR REMARK 3 S11: 0.0248 S12: -0.0059 S13: -0.0210 REMARK 3 S21: -0.0007 S22: 0.0080 S23: -0.0016 REMARK 3 S31: 0.0128 S32: 0.0133 S33: 0.0217 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 772 THROUGH 788 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.3531 -9.3288 15.9310 REMARK 3 T TENSOR REMARK 3 T11: 0.1578 T22: 0.0570 REMARK 3 T33: 0.0999 T12: -0.0609 REMARK 3 T13: -0.0083 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.0016 L22: 0.0038 REMARK 3 L33: 0.0060 L12: 0.0020 REMARK 3 L13: 0.0025 L23: 0.0042 REMARK 3 S TENSOR REMARK 3 S11: -0.0093 S12: -0.0028 S13: 0.0052 REMARK 3 S21: 0.0126 S22: -0.0112 S23: -0.0052 REMARK 3 S31: -0.0084 S32: -0.0012 S33: -0.0112 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 789 THROUGH 823 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7621 -14.9658 24.0383 REMARK 3 T TENSOR REMARK 3 T11: 0.2841 T22: 0.1688 REMARK 3 T33: 0.1502 T12: -0.0667 REMARK 3 T13: -0.0840 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.0007 L22: -0.0000 REMARK 3 L33: 0.0016 L12: 0.0003 REMARK 3 L13: 0.0004 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0203 S12: -0.0093 S13: -0.0048 REMARK 3 S21: 0.0198 S22: 0.0076 S23: -0.0068 REMARK 3 S31: -0.0014 S32: -0.0054 S33: 0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 824 THROUGH 836 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.2730 -28.4557 14.3579 REMARK 3 T TENSOR REMARK 3 T11: 0.1513 T22: 0.1116 REMARK 3 T33: 0.1630 T12: -0.0086 REMARK 3 T13: -0.1194 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.0048 L22: 0.0007 REMARK 3 L33: 0.0015 L12: -0.0020 REMARK 3 L13: -0.0029 L23: 0.0011 REMARK 3 S TENSOR REMARK 3 S11: 0.0055 S12: -0.0016 S13: -0.0082 REMARK 3 S21: 0.0060 S22: 0.0020 S23: -0.0101 REMARK 3 S31: 0.0039 S32: 0.0119 S33: -0.0008 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 837 THROUGH 860 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.6953 -15.7365 19.0649 REMARK 3 T TENSOR REMARK 3 T11: 0.1897 T22: 0.1927 REMARK 3 T33: 0.1980 T12: -0.0406 REMARK 3 T13: -0.1137 T23: -0.0566 REMARK 3 L TENSOR REMARK 3 L11: 0.0018 L22: 0.0126 REMARK 3 L33: 0.0137 L12: -0.0025 REMARK 3 L13: -0.0021 L23: 0.0075 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: -0.0029 S13: -0.0116 REMARK 3 S21: 0.0311 S22: -0.0077 S23: -0.0228 REMARK 3 S31: -0.0231 S32: 0.0148 S33: 0.0107 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 6IWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23729 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 17.50 REMARK 200 R MERGE FOR SHELL (I) : 2.30300 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 2.6.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 0.2 M MGSO4, 20% PEG REMARK 280 3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 44.00667 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 88.01333 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 88.01333 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 44.00667 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 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 514 REMARK 465 GLY A 515 REMARK 465 SER A 516 REMARK 465 SER A 517 REMARK 465 HIS A 518 REMARK 465 HIS A 519 REMARK 465 HIS A 520 REMARK 465 HIS A 521 REMARK 465 HIS A 522 REMARK 465 HIS A 523 REMARK 465 SER A 524 REMARK 465 SER A 525 REMARK 465 GLY A 526 REMARK 465 LEU A 527 REMARK 465 VAL A 528 REMARK 465 PRO A 529 REMARK 465 ARG A 530 REMARK 465 GLY A 531 REMARK 465 SER A 532 REMARK 465 HIS A 533 REMARK 465 MET A 534 REMARK 465 GLU A 535 REMARK 465 SER A 663 REMARK 465 TYR A 664 REMARK 465 ILE A 665 REMARK 465 GLN A 666 REMARK 465 ARG A 667 REMARK 465 SER A 668 REMARK 465 GLU A 669 REMARK 465 HIS A 670 REMARK 465 PRO A 671 REMARK 465 LEU A 672 REMARK 465 ALA A 673 REMARK 465 GLN A 674 REMARK 465 LEU A 675 REMARK 465 TYR A 676 REMARK 465 CYS A 677 REMARK 465 GLY A 790 REMARK 465 ASP A 791 REMARK 465 ARG A 792 REMARK 465 GLU A 793 REMARK 465 ARG A 794 REMARK 465 LYS A 795 REMARK 465 GLU A 796 REMARK 465 LEU A 797 REMARK 465 ASN A 798 REMARK 465 ILE A 799 REMARK 465 GLU A 800 REMARK 465 PRO A 801 REMARK 465 THR A 802 REMARK 465 ASP A 803 REMARK 465 LEU A 804 REMARK 465 MET A 805 REMARK 465 ASN A 806 REMARK 465 ARG A 807 REMARK 465 GLU A 808 REMARK 465 LYS A 809 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 538 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 591 CG CD CE NZ REMARK 470 ARG A 597 CZ NH1 NH2 REMARK 470 LYS A 604 CG CD CE NZ REMARK 470 LYS A 608 CG CD CE NZ REMARK 470 ARG A 658 NE CZ NH1 NH2 REMARK 470 ASN A 662 CG OD1 ND2 REMARK 470 HIS A 678 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 680 CD1 REMARK 470 ILE A 706 CD1 REMARK 470 LYS A 714 CG CD CE NZ REMARK 470 LYS A 730 CG CD CE NZ REMARK 470 ARG A 731 CZ NH1 NH2 REMARK 470 ILE A 739 CD1 REMARK 470 ASN A 742 CG OD1 ND2 REMARK 470 GLU A 747 CG CD OE1 OE2 REMARK 470 LYS A 810 CG CD CE NZ REMARK 470 LYS A 812 CE NZ REMARK 470 GLU A 837 CG CD OE1 OE2 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 LYS A 630 -75.16 -81.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1144 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A1145 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A1146 DISTANCE = 7.28 ANGSTROMS 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 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 617 NE2 REMARK 620 2 HIS A 653 NE2 94.5 REMARK 620 3 ASP A 654 OD2 89.3 82.3 REMARK 620 4 ASP A 764 OD1 87.4 85.3 166.9 REMARK 620 5 HOH A1028 O 88.9 175.1 101.3 91.3 REMARK 620 6 HOH A1065 O 162.0 101.8 85.4 101.4 75.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 900 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 654 OD1 REMARK 620 2 HOH A1014 O 152.9 REMARK 620 3 HOH A1019 O 78.0 82.6 REMARK 620 4 HOH A1046 O 105.8 93.7 92.3 REMARK 620 5 HOH A1065 O 85.1 75.6 88.6 169.0 REMARK 620 6 HOH A1093 O 92.7 96.8 154.2 113.4 66.5 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 MG A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B0C A 902 DBREF 6IWI A 535 860 UNP O76074 PDE5A_HUMAN 535 860 SEQADV 6IWI MET A 514 UNP O76074 EXPRESSION TAG SEQADV 6IWI GLY A 515 UNP O76074 EXPRESSION TAG SEQADV 6IWI SER A 516 UNP O76074 EXPRESSION TAG SEQADV 6IWI SER A 517 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 518 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 519 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 520 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 521 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 522 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 523 UNP O76074 EXPRESSION TAG SEQADV 6IWI SER A 524 UNP O76074 EXPRESSION TAG SEQADV 6IWI SER A 525 UNP O76074 EXPRESSION TAG SEQADV 6IWI GLY A 526 UNP O76074 EXPRESSION TAG SEQADV 6IWI LEU A 527 UNP O76074 EXPRESSION TAG SEQADV 6IWI VAL A 528 UNP O76074 EXPRESSION TAG SEQADV 6IWI PRO A 529 UNP O76074 EXPRESSION TAG SEQADV 6IWI ARG A 530 UNP O76074 EXPRESSION TAG SEQADV 6IWI GLY A 531 UNP O76074 EXPRESSION TAG SEQADV 6IWI SER A 532 UNP O76074 EXPRESSION TAG SEQADV 6IWI HIS A 533 UNP O76074 EXPRESSION TAG SEQADV 6IWI MET A 534 UNP O76074 EXPRESSION TAG SEQRES 1 A 347 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 347 LEU VAL PRO ARG GLY SER HIS MET GLU GLU THR ARG GLU SEQRES 3 A 347 LEU GLN SER LEU ALA ALA ALA VAL VAL PRO SER ALA GLN SEQRES 4 A 347 THR LEU LYS ILE THR ASP PHE SER PHE SER ASP PHE GLU SEQRES 5 A 347 LEU SER ASP LEU GLU THR ALA LEU CYS THR ILE ARG MET SEQRES 6 A 347 PHE THR ASP LEU ASN LEU VAL GLN ASN PHE GLN MET LYS SEQRES 7 A 347 HIS GLU VAL LEU CYS ARG TRP ILE LEU SER VAL LYS LYS SEQRES 8 A 347 ASN TYR ARG LYS ASN VAL ALA TYR HIS ASN TRP ARG HIS SEQRES 9 A 347 ALA PHE ASN THR ALA GLN CYS MET PHE ALA ALA LEU LYS SEQRES 10 A 347 ALA GLY LYS ILE GLN ASN LYS LEU THR ASP LEU GLU ILE SEQRES 11 A 347 LEU ALA LEU LEU ILE ALA ALA LEU SER HIS ASP LEU ASP SEQRES 12 A 347 HIS ARG GLY VAL ASN ASN SER TYR ILE GLN ARG SER GLU SEQRES 13 A 347 HIS PRO LEU ALA GLN LEU TYR CYS HIS SER ILE MET GLU SEQRES 14 A 347 HIS HIS HIS PHE ASP GLN CYS LEU MET ILE LEU ASN SER SEQRES 15 A 347 PRO GLY ASN GLN ILE LEU SER GLY LEU SER ILE GLU GLU SEQRES 16 A 347 TYR LYS THR THR LEU LYS ILE ILE LYS GLN ALA ILE LEU SEQRES 17 A 347 ALA THR ASP LEU ALA LEU TYR ILE LYS ARG ARG GLY GLU SEQRES 18 A 347 PHE PHE GLU LEU ILE ARG LYS ASN GLN PHE ASN LEU GLU SEQRES 19 A 347 ASP PRO HIS GLN LYS GLU LEU PHE LEU ALA MET LEU MET SEQRES 20 A 347 THR ALA CYS ASP LEU SER ALA ILE THR LYS PRO TRP PRO SEQRES 21 A 347 ILE GLN GLN ARG ILE ALA GLU LEU VAL ALA THR GLU PHE SEQRES 22 A 347 PHE ASP GLN GLY ASP ARG GLU ARG LYS GLU LEU ASN ILE SEQRES 23 A 347 GLU PRO THR ASP LEU MET ASN ARG GLU LYS LYS ASN LYS SEQRES 24 A 347 ILE PRO SER MET GLN VAL GLY PHE ILE ASP ALA ILE CYS SEQRES 25 A 347 LEU GLN LEU TYR GLU ALA LEU THR HIS VAL SER GLU ASP SEQRES 26 A 347 CYS PHE PRO LEU LEU ASP GLY CYS ARG LYS ASN ARG GLN SEQRES 27 A 347 LYS TRP GLN ALA LEU ALA GLU GLN GLN HET MG A 900 1 HET ZN A 901 1 HET B0C A 902 32 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM B0C N-[3-(4,5-DIETHYL-6-OXO-1,6-DIHYDROPYRIMIDIN-2-YL)-4- HETNAM 2 B0C PROPOXYPHENYL]-2-(4-METHYLPIPERAZIN-1-YL)ACETAMIDE FORMUL 2 MG MG 2+ FORMUL 3 ZN ZN 2+ FORMUL 4 B0C C24 H35 N5 O3 FORMUL 5 HOH *146(H2 O) HELIX 1 AA1 THR A 537 ALA A 546 1 10 HELIX 2 AA2 SER A 550 LYS A 555 1 6 HELIX 3 AA3 SER A 567 LEU A 582 1 16 HELIX 4 AA4 ASN A 583 GLN A 589 1 7 HELIX 5 AA5 LYS A 591 ASN A 605 1 15 HELIX 6 AA6 ASN A 614 ALA A 631 1 18 HELIX 7 AA7 ILE A 634 LEU A 638 5 5 HELIX 8 AA8 THR A 639 HIS A 653 1 15 HELIX 9 AA9 SER A 679 SER A 695 1 17 HELIX 10 AB1 SER A 705 THR A 723 1 19 HELIX 11 AB2 ASP A 724 LYS A 741 1 18 HELIX 12 AB3 ASP A 748 LEU A 765 1 18 HELIX 13 AB4 SER A 766 LYS A 770 5 5 HELIX 14 AB5 PRO A 771 GLN A 789 1 19 HELIX 15 AB6 LYS A 812 ILE A 824 1 13 HELIX 16 AB7 ILE A 824 SER A 836 1 13 HELIX 17 AB8 CYS A 839 GLN A 859 1 21 LINK NE2 HIS A 617 ZN ZN A 901 1555 1555 2.20 LINK NE2 HIS A 653 ZN ZN A 901 1555 1555 2.20 LINK OD1 ASP A 654 MG MG A 900 1555 1555 2.39 LINK OD2 ASP A 654 ZN ZN A 901 1555 1555 2.20 LINK OD1 ASP A 764 ZN ZN A 901 1555 1555 2.21 LINK MG MG A 900 O HOH A1014 1555 1555 2.14 LINK MG MG A 900 O HOH A1019 1555 1555 2.18 LINK MG MG A 900 O HOH A1046 1555 1555 2.04 LINK MG MG A 900 O HOH A1065 1555 1555 2.31 LINK MG MG A 900 O HOH A1093 1555 1555 2.03 LINK ZN ZN A 901 O HOH A1028 1555 1555 2.44 LINK ZN ZN A 901 O HOH A1065 1555 1555 2.46 SITE 1 AC1 7 ASP A 654 GLU A 682 HOH A1014 HOH A1019 SITE 2 AC1 7 HOH A1046 HOH A1065 HOH A1093 SITE 1 AC2 6 HIS A 617 HIS A 653 ASP A 654 ASP A 764 SITE 2 AC2 6 HOH A1028 HOH A1065 SITE 1 AC3 8 TYR A 612 ALA A 779 PHE A 786 GLN A 817 SITE 2 AC3 8 GLY A 819 PHE A 820 HOH A1015 HOH A1018 CRYST1 74.748 74.748 132.020 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 0.013378 0.007724 0.000000 0.00000 SCALE2 0.000000 0.015448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007575 0.00000