PDB Short entry for 4PM0 HEADER HYDROLASE 20-MAY-14 4PM0 TITLE PDE7A CATALYTIC DOMAIN IN COMPLEX WITH 2-(CYCLOPENTYLAMINO)THIENO[3,2- TITLE 2 D]PYRIMIDIN-4(3H)-ONE DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE COMPND 3 7A; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 130-482; COMPND 6 SYNONYM: HCP1,TM22; COMPND 7 EC: 3.1.4.53; COMPND 8 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: PDE7A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS KEYWDS PHOSPHODIESTERASE, PDE7, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KAWAI,Y.ENDO,T.ASANO,S.AMANO,K.SAWADA,N.UEO,N.TAKAHASHI,Y.SONODA, AUTHOR 2 N.KAMEI,N.NAGATA REVDAT 4 08-NOV-23 4PM0 1 LINK REVDAT 3 27-SEP-17 4PM0 1 SOURCE JRNL REMARK REVDAT 2 24-DEC-14 4PM0 1 JRNL REVDAT 1 03-DEC-14 4PM0 0 JRNL AUTH K.KAWAI,Y.ENDO,T.ASANO,S.AMANO,K.SAWADA,N.UEO,N.TAKAHASHI, JRNL AUTH 2 Y.SONODA,M.NAGAI,N.KAMEI,N.NAGATA JRNL TITL DISCOVERY OF JRNL TITL 2 2-(CYCLOPENTYLAMINO)THIENO[3,2-D]PYRIMIDIN-4(3H)-ONE JRNL TITL 3 DERIVATIVES AS A NEW SERIES OF POTENT PHOSPHODIESTERASE 7 JRNL TITL 4 INHIBITORS. JRNL REF J.MED.CHEM. V. 57 9844 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 25383422 JRNL DOI 10.1021/JM5008215 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 25982 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1417 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2013 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2595 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : 0.02000 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): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.041 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2685 ; 0.024 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3640 ; 1.757 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 317 ; 5.770 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;38.371 ;23.731 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 460 ;15.174 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;25.275 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2041 ; 0.010 ; 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): 1584 ; 1.156 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2553 ; 2.104 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1101 ; 3.553 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1087 ; 5.428 ; 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 4PM0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000200770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29559 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 29.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: 1ZKL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 - 0.8M (NH4)2SO4, 3MM REMARK 280 MERCAPTOETHANOL, 10MM MGCL2, 10MM EDTA, 0.1M TRIS HCL, PH 7.5,, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 21.48600 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 42.97200 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 42.97200 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 21.48600 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 GLY A 94 REMARK 465 SER A 95 REMARK 465 GLY A 96 REMARK 465 MET A 97 REMARK 465 LYS A 98 REMARK 465 GLU A 99 REMARK 465 THR A 100 REMARK 465 ALA A 101 REMARK 465 ALA A 102 REMARK 465 ALA A 103 REMARK 465 LYS A 104 REMARK 465 PRO A 105 REMARK 465 GLU A 106 REMARK 465 ARG A 107 REMARK 465 GLN A 108 REMARK 465 HIS A 109 REMARK 465 MET A 110 REMARK 465 ASP A 111 REMARK 465 SER A 112 REMARK 465 PRO A 113 REMARK 465 ASP A 114 REMARK 465 LEU A 115 REMARK 465 GLY A 116 REMARK 465 THR A 117 REMARK 465 ASP A 118 REMARK 465 ASP A 119 REMARK 465 ASP A 120 REMARK 465 ASP A 121 REMARK 465 LYS A 122 REMARK 465 ALA A 123 REMARK 465 MET A 124 REMARK 465 ALA A 125 REMARK 465 ASP A 126 REMARK 465 ILE A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 SER A 130 REMARK 465 ASN A 131 REMARK 465 SER A 132 REMARK 465 LEU A 133 REMARK 465 ASN A 134 REMARK 465 ILE A 135 REMARK 465 LEU A 136 REMARK 465 ASP A 137 REMARK 465 ASP A 138 REMARK 465 GLU A 457 REMARK 465 GLN A 458 REMARK 465 SER A 459 REMARK 465 SER A 460 REMARK 465 SER A 461 REMARK 465 GLU A 462 REMARK 465 ASP A 463 REMARK 465 THR A 464 REMARK 465 ASP A 465 REMARK 465 ALA A 466 REMARK 465 ALA A 467 REMARK 465 PHE A 468 REMARK 465 GLU A 469 REMARK 465 LEU A 470 REMARK 465 ASN A 471 REMARK 465 SER A 472 REMARK 465 GLN A 473 REMARK 465 LEU A 474 REMARK 465 LEU A 475 REMARK 465 PRO A 476 REMARK 465 GLN A 477 REMARK 465 GLU A 478 REMARK 465 ASN A 479 REMARK 465 ARG A 480 REMARK 465 LEU A 481 REMARK 465 SER A 482 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 NE2 GLN A 208 O HOH A 753 2.00 REMARK 500 ND2 ASN A 155 O HOH A 747 2.10 REMARK 500 NH2 ARG A 163 O HOH A 726 2.16 REMARK 500 O HOH A 780 O HOH A 817 2.19 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 ARG A 163 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 163 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 MET A 200 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 350 NE - CZ - NH1 ANGL. DEV. = 3.2 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 PHE A 156 135.62 -39.30 REMARK 500 ASN A 166 48.06 38.88 REMARK 500 ASN A 277 18.53 56.82 REMARK 500 LEU A 401 -2.06 78.65 REMARK 500 GLN A 455 -149.45 -92.17 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 A 760 DISTANCE = 7.15 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 216 NE2 REMARK 620 2 HIS A 252 NE2 91.0 REMARK 620 3 ASP A 253 OD2 85.1 87.3 REMARK 620 4 ASP A 362 OD1 93.7 90.6 177.6 REMARK 620 5 HOH A 672 O 89.5 177.4 95.4 86.7 REMARK 620 6 HOH A 834 O 165.7 102.1 90.0 91.6 77.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 253 OD1 REMARK 620 2 HOH A 673 O 100.8 REMARK 620 3 HOH A 674 O 93.5 88.4 REMARK 620 4 HOH A 675 O 166.8 92.3 85.5 REMARK 620 5 HOH A 676 O 82.7 176.4 90.8 84.1 REMARK 620 6 HOH A 834 O 92.7 85.7 172.2 89.6 94.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 32V A 503 DBREF 4PM0 A 130 482 UNP Q13946 PDE7A_HUMAN 130 482 SEQADV 4PM0 GLY A 94 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 SER A 95 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 GLY A 96 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 MET A 97 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 LYS A 98 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 GLU A 99 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 THR A 100 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ALA A 101 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ALA A 102 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ALA A 103 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 LYS A 104 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 PRO A 105 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 GLU A 106 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ARG A 107 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 GLN A 108 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 HIS A 109 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 MET A 110 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 111 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 SER A 112 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 PRO A 113 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 114 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 LEU A 115 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 GLY A 116 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 THR A 117 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 118 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 119 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 120 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 121 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 LYS A 122 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ALA A 123 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 MET A 124 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ALA A 125 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ASP A 126 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 ILE A 127 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 GLY A 128 UNP Q13946 EXPRESSION TAG SEQADV 4PM0 SER A 129 UNP Q13946 EXPRESSION TAG SEQRES 1 A 389 GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PRO GLU SEQRES 2 A 389 ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP ASP SEQRES 3 A 389 ASP ASP LYS ALA MET ALA ASP ILE GLY SER SER ASN SER SEQRES 4 A 389 LEU ASN ILE LEU ASP ASP ASP TYR ASN GLY GLN ALA LYS SEQRES 5 A 389 CYS MET LEU GLU LYS VAL GLY ASN TRP ASN PHE ASP ILE SEQRES 6 A 389 PHE LEU PHE ASP ARG LEU THR ASN GLY ASN SER LEU VAL SEQRES 7 A 389 SER LEU THR PHE HIS LEU PHE SER LEU HIS GLY LEU ILE SEQRES 8 A 389 GLU TYR PHE HIS LEU ASP MET MET LYS LEU ARG ARG PHE SEQRES 9 A 389 LEU VAL MET ILE GLN GLU ASP TYR HIS SER GLN ASN PRO SEQRES 10 A 389 TYR HIS ASN ALA VAL HIS ALA ALA ASP VAL THR GLN ALA SEQRES 11 A 389 MET HIS CYS TYR LEU LYS GLU PRO LYS LEU ALA ASN SER SEQRES 12 A 389 VAL THR PRO TRP ASP ILE LEU LEU SER LEU ILE ALA ALA SEQRES 13 A 389 ALA THR HIS ASP LEU ASP HIS PRO GLY VAL ASN GLN PRO SEQRES 14 A 389 PHE LEU ILE LYS THR ASN HIS TYR LEU ALA THR LEU TYR SEQRES 15 A 389 LYS ASN THR SER VAL LEU GLU ASN HIS HIS TRP ARG SER SEQRES 16 A 389 ALA VAL GLY LEU LEU ARG GLU SER GLY LEU PHE SER HIS SEQRES 17 A 389 LEU PRO LEU GLU SER ARG GLN GLN MET GLU THR GLN ILE SEQRES 18 A 389 GLY ALA LEU ILE LEU ALA THR ASP ILE SER ARG GLN ASN SEQRES 19 A 389 GLU TYR LEU SER LEU PHE ARG SER HIS LEU ASP ARG GLY SEQRES 20 A 389 ASP LEU CYS LEU GLU ASP THR ARG HIS ARG HIS LEU VAL SEQRES 21 A 389 LEU GLN MET ALA LEU LYS CYS ALA ASP ILE CYS ASN PRO SEQRES 22 A 389 CYS ARG THR TRP GLU LEU SER LYS GLN TRP SER GLU LYS SEQRES 23 A 389 VAL THR GLU GLU PHE PHE HIS GLN GLY ASP ILE GLU LYS SEQRES 24 A 389 LYS TYR HIS LEU GLY VAL SER PRO LEU CYS ASP ARG HIS SEQRES 25 A 389 THR GLU SER ILE ALA ASN ILE GLN ILE GLY PHE MET THR SEQRES 26 A 389 TYR LEU VAL GLU PRO LEU PHE THR GLU TRP ALA ARG PHE SEQRES 27 A 389 SER ASN THR ARG LEU SER GLN THR MET LEU GLY HIS VAL SEQRES 28 A 389 GLY LEU ASN LYS ALA SER TRP LYS GLY LEU GLN ARG GLU SEQRES 29 A 389 GLN SER SER SER GLU ASP THR ASP ALA ALA PHE GLU LEU SEQRES 30 A 389 ASN SER GLN LEU LEU PRO GLN GLU ASN ARG LEU SER HET ZN A 501 1 HET MG A 502 1 HET 32V A 503 20 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 32V 2-(CYCLOPENTYLAMINO)-3-ETHYL-7-ETHYNYLTHIENO[3,2- HETNAM 2 32V D]PYRIMIDIN-4(3H)-ONE FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 32V C15 H17 N3 O S FORMUL 5 HOH *238(H2 O) HELIX 1 AA1 ASP A 139 GLU A 149 1 11 HELIX 2 AA2 ASP A 157 THR A 165 1 9 HELIX 3 AA3 ASN A 168 HIS A 181 1 14 HELIX 4 AA4 GLY A 182 PHE A 187 1 6 HELIX 5 AA5 ASP A 190 ASP A 204 1 15 HELIX 6 AA6 ASN A 213 LYS A 229 1 17 HELIX 7 AA7 GLU A 230 ASN A 235 1 6 HELIX 8 AA8 THR A 238 HIS A 252 1 15 HELIX 9 AA9 ASN A 260 THR A 267 1 8 HELIX 10 AB1 HIS A 269 TYR A 275 1 7 HELIX 11 AB2 SER A 279 GLY A 297 1 19 HELIX 12 AB3 PRO A 303 ALA A 320 1 18 HELIX 13 AB4 THR A 321 SER A 324 5 4 HELIX 14 AB5 ARG A 325 GLY A 340 1 16 HELIX 15 AB6 ASP A 346 ILE A 363 1 18 HELIX 16 AB7 CYS A 364 ARG A 368 5 5 HELIX 17 AB8 THR A 369 TYR A 394 1 26 HELIX 18 AB9 SER A 408 LEU A 420 1 13 HELIX 19 AC1 LEU A 420 SER A 432 1 13 HELIX 20 AC2 THR A 434 LEU A 454 1 21 LINK NE2 HIS A 216 ZN ZN A 501 1555 1555 2.27 LINK NE2 HIS A 252 ZN ZN A 501 1555 1555 2.26 LINK OD2 ASP A 253 ZN ZN A 501 1555 1555 2.08 LINK OD1 ASP A 253 MG MG A 502 1555 1555 2.01 LINK OD1 ASP A 362 ZN ZN A 501 1555 1555 2.20 LINK ZN ZN A 501 O HOH A 672 1555 1555 2.43 LINK ZN ZN A 501 O HOH A 834 1555 1555 2.24 LINK MG MG A 502 O HOH A 673 1555 1555 2.20 LINK MG MG A 502 O HOH A 674 1555 1555 2.07 LINK MG MG A 502 O HOH A 675 1555 1555 2.13 LINK MG MG A 502 O HOH A 676 1555 1555 2.10 LINK MG MG A 502 O HOH A 834 1555 1555 1.97 SITE 1 AC1 6 HIS A 216 HIS A 252 ASP A 253 ASP A 362 SITE 2 AC1 6 HOH A 672 HOH A 834 SITE 1 AC2 6 ASP A 253 HOH A 673 HOH A 674 HOH A 675 SITE 2 AC2 6 HOH A 676 HOH A 834 SITE 1 AC3 8 TYR A 211 ILE A 363 ASN A 365 VAL A 380 SITE 2 AC3 8 ILE A 412 GLN A 413 PHE A 416 HOH A 698 CRYST1 116.187 116.187 64.458 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 0.008607 0.004969 0.000000 0.00000 SCALE2 0.000000 0.009938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015514 0.00000