HEADER HYDROLASE 15-NOV-17 6EZF TITLE PDE2 IN COMPLEX WITH MOLECULE 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-DEPENDENT 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYCLIC GMP-STIMULATED PHOSPHODIESTERASE,CGSPDE; COMPND 5 EC: 3.1.4.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS PDE2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.TRESADERN,L.PEREZ-BENITO,H.KERAENEN,H.VAN VLIJMEN REVDAT 2 08-MAY-19 6EZF 1 LINK REVDAT 1 04-APR-18 6EZF 0 JRNL AUTH L.PEREZ-BENITO,H.KERANEN,H.VAN VLIJMEN,G.TRESADERN JRNL TITL PREDICTING BINDING FREE ENERGIES OF PDE2 INHIBITORS. THE JRNL TITL 2 DIFFICULTIES OF PROTEIN CONFORMATION. JRNL REF SCI REP V. 8 4883 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 29559702 JRNL DOI 10.1038/S41598-018-23039-5 REMARK 2 REMARK 2 RESOLUTION. 1.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 58498 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.600 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3837 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 347 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : 0.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.755 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3103 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2121 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4224 ; 1.128 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5143 ; 1.391 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 5.024 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;34.557 ;23.867 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 544 ;11.963 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.993 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3562 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 664 ; 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): 1869 ; 1.932 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 736 ; 0.875 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3048 ; 2.741 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1234 ; 4.132 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1174 ; 5.719 ; 6.000 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): 5224 ; 1.678 ; 3.000 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 : NULL 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 6EZF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60146 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 55.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.980 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 (%): 48.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG4000 0.10 M TRIS 8.25 0.20 M REMARK 280 LISO4, PH 8.25, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 27.11950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.19550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.65750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.19550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.11950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.65750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 575 REMARK 465 HIS A 576 REMARK 465 ALA A 577 REMARK 465 SER A 578 REMARK 465 ASP A 579 REMARK 465 HIS A 922 REMARK 465 HIS A 923 REMARK 465 HIS A 924 REMARK 465 HIS A 925 REMARK 465 HIS A 926 REMARK 465 HIS A 927 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 584 CG CD CE NZ REMARK 480 ASP A 588 CG OD1 OD2 REMARK 480 GLN A 591 CD OE1 NE2 REMARK 480 LYS A 633 CE NZ REMARK 480 ARG A 701 CZ NH1 NH2 REMARK 480 GLU A 722 CD OE1 OE2 REMARK 480 ARG A 751 CD NE CZ NH1 NH2 REMARK 480 LYS A 752 CD CE NZ REMARK 480 LEU A 770 CD1 CD2 REMARK 480 LYS A 782 CD CE NZ REMARK 480 GLU A 785 CD OE1 OE2 REMARK 480 LYS A 793 CD CE NZ REMARK 480 GLN A 794 CD OE1 NE2 REMARK 480 LYS A 817 NZ REMARK 480 LYS A 872 CE NZ REMARK 480 GLU A 893 CD OE1 OE2 REMARK 480 GLU A 921 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 ASP A 597 141.67 -170.00 REMARK 500 ASP A 597 141.28 -170.00 REMARK 500 VAL A 725 66.70 61.52 REMARK 500 VAL A 725 68.00 61.52 REMARK 500 LYS A 814 -149.94 -96.60 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 A1447 DISTANCE = 11.05 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 A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 660 NE2 REMARK 620 2 HIS A 696 NE2 93.5 REMARK 620 3 ASP A 697 OD2 87.9 84.0 REMARK 620 4 ASP A 808 OD1 87.9 89.1 171.6 REMARK 620 5 HOH A1181 O 170.0 96.5 92.4 93.0 REMARK 620 6 HOH A1302 O 86.4 177.3 98.8 88.2 83.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 697 OD1 REMARK 620 2 HOH A1131 O 81.2 REMARK 620 3 HOH A1181 O 94.8 97.8 REMARK 620 4 HOH A1216 O 164.4 84.9 94.1 REMARK 620 5 HOH A1275 O 87.6 88.5 173.5 85.0 REMARK 620 6 HOH A1376 O 102.7 172.7 88.0 90.4 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1007 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1302 O REMARK 620 2 HOH A1376 O 103.6 REMARK 620 N 1 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C6Z A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1007 DBREF 6EZF A 578 919 UNP O00408 PDE2A_HUMAN 322 663 SEQADV 6EZF MET A 575 UNP O00408 INITIATING METHIONINE SEQADV 6EZF HIS A 576 UNP O00408 EXPRESSION TAG SEQADV 6EZF ALA A 577 UNP O00408 EXPRESSION TAG SEQADV 6EZF LEU A 920 UNP O00408 EXPRESSION TAG SEQADV 6EZF GLU A 921 UNP O00408 EXPRESSION TAG SEQADV 6EZF HIS A 922 UNP O00408 EXPRESSION TAG SEQADV 6EZF HIS A 923 UNP O00408 EXPRESSION TAG SEQADV 6EZF HIS A 924 UNP O00408 EXPRESSION TAG SEQADV 6EZF HIS A 925 UNP O00408 EXPRESSION TAG SEQADV 6EZF HIS A 926 UNP O00408 EXPRESSION TAG SEQADV 6EZF HIS A 927 UNP O00408 EXPRESSION TAG SEQRES 1 A 353 MET HIS ALA SER ASP ASP GLU TYR THR LYS LEU LEU HIS SEQRES 2 A 353 ASP GLY ILE GLN PRO VAL ALA ALA ILE ASP SER ASN PHE SEQRES 3 A 353 ALA SER PHE THR TYR THR PRO ARG SER LEU PRO GLU ASP SEQRES 4 A 353 ASP THR SER MET ALA ILE LEU SER MET LEU GLN ASP MET SEQRES 5 A 353 ASN PHE ILE ASN ASN TYR LYS ILE ASP CYS PRO THR LEU SEQRES 6 A 353 ALA ARG PHE CYS LEU MET VAL LYS LYS GLY TYR ARG ASP SEQRES 7 A 353 PRO PRO TYR HIS ASN TRP MET HIS ALA PHE SER VAL SER SEQRES 8 A 353 HIS PHE CYS TYR LEU LEU TYR LYS ASN LEU GLU LEU THR SEQRES 9 A 353 ASN TYR LEU GLU ASP ILE GLU ILE PHE ALA LEU PHE ILE SEQRES 10 A 353 SER CYS MET CYS HIS ASP LEU ASP HIS ARG GLY THR ASN SEQRES 11 A 353 ASN SER PHE GLN VAL ALA SER LYS SER VAL LEU ALA ALA SEQRES 12 A 353 LEU TYR SER SER GLU GLY SER VAL MET GLU ARG HIS HIS SEQRES 13 A 353 PHE ALA GLN ALA ILE ALA ILE LEU ASN THR HIS GLY CYS SEQRES 14 A 353 ASN ILE PHE ASP HIS PHE SER ARG LYS ASP TYR GLN ARG SEQRES 15 A 353 MET LEU ASP LEU MET ARG ASP ILE ILE LEU ALA THR ASP SEQRES 16 A 353 LEU ALA HIS HIS LEU ARG ILE PHE LYS ASP LEU GLN LYS SEQRES 17 A 353 MET ALA GLU VAL GLY TYR ASP ARG ASN ASN LYS GLN HIS SEQRES 18 A 353 HIS ARG LEU LEU LEU CYS LEU LEU MET THR SER CYS ASP SEQRES 19 A 353 LEU SER ASP GLN THR LYS GLY TRP LYS THR THR ARG LYS SEQRES 20 A 353 ILE ALA GLU LEU ILE TYR LYS GLU PHE PHE SER GLN GLY SEQRES 21 A 353 ASP LEU GLU LYS ALA MET GLY ASN ARG PRO MET GLU MET SEQRES 22 A 353 MET ASP ARG GLU LYS ALA TYR ILE PRO GLU LEU GLN ILE SEQRES 23 A 353 SER PHE MET GLU HIS ILE ALA MET PRO ILE TYR LYS LEU SEQRES 24 A 353 LEU GLN ASP LEU PHE PRO LYS ALA ALA GLU LEU TYR GLU SEQRES 25 A 353 ARG VAL ALA SER ASN ARG GLU HIS TRP THR LYS VAL SER SEQRES 26 A 353 HIS LYS PHE THR ILE ARG GLY LEU PRO SER ASN ASN SER SEQRES 27 A 353 LEU ASP PHE LEU ASP GLU GLU LEU GLU HIS HIS HIS HIS SEQRES 28 A 353 HIS HIS HET MG A1001 1 HET ZN A1002 1 HET C6Z A1003 16 HET GOL A1004 12 HET GOL A1005 6 HET SO4 A1006 5 HET NA A1007 1 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM C6Z 6-[(2,4-DICHLOROPHENYL)METHYL]PYRIDAZINE-3-THIOL HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 ZN ZN 2+ FORMUL 4 C6Z C11 H8 CL2 N2 S FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 SO4 O4 S 2- FORMUL 8 NA NA 1+ FORMUL 9 HOH *347(H2 O) HELIX 1 AA1 ASP A 580 ASP A 588 1 9 HELIX 2 AA2 PRO A 592 ILE A 596 5 5 HELIX 3 AA3 THR A 606 LEU A 610 5 5 HELIX 4 AA4 PRO A 611 ASP A 613 5 3 HELIX 5 AA5 ASP A 614 MET A 626 1 13 HELIX 6 AA6 ASN A 627 TYR A 632 1 6 HELIX 7 AA7 ASP A 635 GLY A 649 1 15 HELIX 8 AA8 ASN A 657 GLU A 676 1 20 HELIX 9 AA9 LEU A 677 TYR A 680 5 4 HELIX 10 AB1 GLU A 682 HIS A 696 1 15 HELIX 11 AB2 SER A 713 SER A 720 1 8 HELIX 12 AB3 MET A 726 ASN A 739 1 14 HELIX 13 AB4 SER A 750 ALA A 767 1 18 HELIX 14 AB5 ASP A 769 GLY A 787 1 19 HELIX 15 AB6 ASN A 792 LEU A 809 1 18 HELIX 16 AB7 SER A 810 LYS A 814 5 5 HELIX 17 AB8 GLY A 815 MET A 840 1 26 HELIX 18 AB9 MET A 845 ASP A 849 5 5 HELIX 19 AC1 TYR A 854 ILE A 866 1 13 HELIX 20 AC2 ILE A 866 PHE A 878 1 13 HELIX 21 AC3 ALA A 881 PHE A 902 1 22 HELIX 22 AC4 ASP A 914 GLU A 921 1 8 LINK NE2 HIS A 660 ZN ZN A1002 1555 1555 2.17 LINK NE2 HIS A 696 ZN ZN A1002 1555 1555 2.21 LINK OD1 ASP A 697 MG MG A1001 1555 1555 2.12 LINK OD2 ASP A 697 ZN ZN A1002 1555 1555 2.13 LINK OD1 ASP A 808 ZN ZN A1002 1555 1555 2.15 LINK MG MG A1001 O HOH A1131 1555 1555 2.16 LINK MG MG A1001 O HOH A1181 1555 1555 2.10 LINK MG MG A1001 O HOH A1216 1555 1555 2.09 LINK MG MG A1001 O HOH A1275 1555 1555 2.21 LINK MG MG A1001 O HOH A1376 1555 1555 2.00 LINK ZN ZN A1002 O HOH A1181 1555 1555 2.06 LINK ZN ZN A1002 O HOH A1302 1555 1555 2.22 LINK NA NA A1007 O HOH A1302 1555 1555 1.92 LINK NA NA A1007 O HOH A1376 1555 1555 2.08 SITE 1 AC1 6 ASP A 697 HOH A1131 HOH A1181 HOH A1216 SITE 2 AC1 6 HOH A1275 HOH A1376 SITE 1 AC2 6 HIS A 660 HIS A 696 ASP A 697 ASP A 808 SITE 2 AC2 6 HOH A1181 HOH A1302 SITE 1 AC3 9 ALA A 717 GLN A 812 ILE A 826 TYR A 827 SITE 2 AC3 9 PHE A 830 MET A 847 GLN A 859 PHE A 862 SITE 3 AC3 9 HOH A1105 SITE 1 AC4 9 TYR A 719 LEU A 774 PHE A 777 HIS A 865 SITE 2 AC4 9 PRO A 869 THR A 903 ARG A 905 HOH A1121 SITE 3 AC4 9 HOH A1130 SITE 1 AC5 7 GLU A 864 LEU A 907 SER A 909 HOH A1111 SITE 2 AC5 7 HOH A1121 HOH A1192 HOH A1303 SITE 1 AC6 8 THR A 606 GLY A 815 THR A 818 HOH A1101 SITE 2 AC6 8 HOH A1106 HOH A1197 HOH A1231 HOH A1244 SITE 1 AC7 3 HIS A 656 HOH A1302 HOH A1376 CRYST1 54.239 65.315 104.391 90.00 90.00 90.00 P 21 21 21 4 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 0.018437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009579 0.00000