PDB Short entry for 3LFV HEADER HYDROLASE 18-JAN-10 3LFV TITLE CRYSTAL STRUCTURE OF UNLIGANDED PDE5A GAF DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 98-518; COMPND 5 SYNONYM: CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, CGB-PDE; COMPND 6 EC: 3.1.4.35; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDE5, PDE5A, PDE5A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(CODONPLUS); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A (MODIFIED) KEYWDS GAF, CGMP SIGNALING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,H.ROBINSON,H.KE REVDAT 2 05-JAN-11 3LFV 1 JRNL REVDAT 1 22-SEP-10 3LFV 0 JRNL AUTH H.WANG,H.ROBINSON,H.KE JRNL TITL CONFORMATION CHANGES, N-TERMINAL INVOLVEMENT, AND CGMP JRNL TITL 2 SIGNAL RELAY IN THE PHOSPHODIESTERASE-5 GAF DOMAIN. JRNL REF J.BIOL.CHEM. V. 285 38149 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20861010 JRNL DOI 10.1074/JBC.M110.141614 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 38161 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2034 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6110 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.60000 REMARK 3 B22 (A**2) : -1.60000 REMARK 3 B33 (A**2) : 2.40000 REMARK 3 B12 (A**2) : -0.80000 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): 0.458 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.325 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.254 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.525 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6210 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8360 ; 0.667 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 762 ;12.467 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 293 ;39.847 ;25.256 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1173 ;24.919 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.834 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 949 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4612 ; 0.019 ; 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): 3841 ; 2.121 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6210 ; 3.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2369 ; 5.302 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2150 ; 8.449 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 3100 ; 0.00 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 3100 ; 0.00 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 3017 ; 0.00 ; 0.50 REMARK 3 MEDIUM THERMAL 2 B (A**2): 3017 ; 0.00 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -14.5211 81.3858 41.4403 REMARK 3 T TENSOR REMARK 3 T11: 0.1498 T22: 0.4415 REMARK 3 T33: 0.2362 T12: 0.0572 REMARK 3 T13: 0.0231 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.0025 L22: 5.3436 REMARK 3 L33: 2.8920 L12: 0.8652 REMARK 3 L13: -0.6873 L23: -2.3319 REMARK 3 S TENSOR REMARK 3 S11: 0.0536 S12: 0.0005 S13: -0.0262 REMARK 3 S21: -0.1493 S22: 0.2326 S23: 0.4831 REMARK 3 S31: -0.4533 S32: -0.4085 S33: -0.2862 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9267 77.5760 34.8941 REMARK 3 T TENSOR REMARK 3 T11: 0.1643 T22: 0.5505 REMARK 3 T33: 0.3276 T12: -0.0375 REMARK 3 T13: 0.1357 T23: 0.0464 REMARK 3 L TENSOR REMARK 3 L11: 1.8142 L22: 5.7749 REMARK 3 L33: 3.1544 L12: -2.1347 REMARK 3 L13: 0.7612 L23: -2.7227 REMARK 3 S TENSOR REMARK 3 S11: 0.1802 S12: 0.2057 S13: 0.2757 REMARK 3 S21: -0.3143 S22: -0.4713 S23: -0.9346 REMARK 3 S31: -0.3496 S32: 0.5762 S33: 0.2911 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 3LFV COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB057226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9796, 0.94, 1.0 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40247 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 21.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE UNLIGANDED PDE5A (20 MG/ML) WAS REMARK 280 CRYSTALLIZED BY VAPOR DIFFUSION AGAINST THE WELL BUFFER OF 10% REMARK 280 PEG3350, 5% MPD, 0.1 M SODIUM CITRATE, PH5.6, 20 MM DTT, VAPOR REMARK 280 DIFFUSION, HANGING 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 44.95567 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 89.91133 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 89.91133 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 44.95567 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 300 REMARK: A DIMER IS LIKELY THE BIOLOGICAL ACTIVE ASSEMBLY. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 128 REMARK 465 GLU A 129 REMARK 465 LYS A 130 REMARK 465 LYS A 131 REMARK 465 GLU A 132 REMARK 465 GLN A 133 REMARK 465 MET A 134 REMARK 465 PRO A 135 REMARK 465 LEU A 136 REMARK 465 THR A 137 REMARK 465 PRO A 138 REMARK 465 PRO A 139 REMARK 465 ARG A 140 REMARK 465 PHE A 141 REMARK 465 ASP A 142 REMARK 465 HIS A 143 REMARK 465 ASP A 144 REMARK 465 GLU A 145 REMARK 465 SER A 395 REMARK 465 ASP A 396 REMARK 465 THR A 397 REMARK 465 LEU A 398 REMARK 465 THR A 399 REMARK 465 ARG A 400 REMARK 465 GLU A 401 REMARK 465 HIS A 402 REMARK 465 ASP A 403 REMARK 465 ALA A 404 REMARK 465 ASN A 405 REMARK 465 LYS A 406 REMARK 465 THR A 436 REMARK 465 THR A 437 REMARK 465 GLU A 438 REMARK 465 ASN A 439 REMARK 465 THR A 440 REMARK 465 GLY A 441 REMARK 465 ASN A 442 REMARK 465 VAL A 443 REMARK 465 ASN A 444 REMARK 465 GLN A 445 REMARK 465 LYS B 131 REMARK 465 GLU B 132 REMARK 465 GLN B 133 REMARK 465 MET B 134 REMARK 465 PRO B 135 REMARK 465 LEU B 136 REMARK 465 THR B 137 REMARK 465 PRO B 138 REMARK 465 PRO B 139 REMARK 465 ARG B 140 REMARK 465 PHE B 141 REMARK 465 ASP B 142 REMARK 465 HIS B 143 REMARK 465 ASP B 144 REMARK 465 GLU B 145 REMARK 465 GLY B 146 REMARK 465 GLU B 209 REMARK 465 GLY B 210 REMARK 465 SER B 211 REMARK 465 THR B 212 REMARK 465 LEU B 213 REMARK 465 GLU B 214 REMARK 465 GLU B 215 REMARK 465 VAL B 216 REMARK 465 SER B 217 REMARK 465 SER B 395 REMARK 465 ASP B 396 REMARK 465 THR B 397 REMARK 465 LEU B 398 REMARK 465 THR B 399 REMARK 465 ARG B 400 REMARK 465 GLU B 401 REMARK 465 HIS B 402 REMARK 465 ASP B 403 REMARK 465 ALA B 404 REMARK 465 ASN B 405 REMARK 465 LYS B 406 REMARK 465 ILE B 407 REMARK 465 ASN B 408 REMARK 465 TRP B 435 REMARK 465 THR B 436 REMARK 465 THR B 437 REMARK 465 GLU B 438 REMARK 465 ASN B 439 REMARK 465 THR B 440 REMARK 465 GLY B 441 REMARK 465 ASN B 442 REMARK 465 VAL B 443 REMARK 465 ASN B 444 REMARK 465 GLN B 445 REMARK 465 GLN B 446 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 SER B 102 N SER B 104 2.02 REMARK 500 O MET B 91 N MET B 94 2.13 REMARK 500 O TYR B 414 OG1 THR B 418 2.16 REMARK 500 ND2 ASN A 327 ND2 ASN B 330 2.16 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 VAL A 115 129.17 178.15 REMARK 500 SER A 118 87.29 62.62 REMARK 500 GLU A 119 7.05 82.22 REMARK 500 SER A 123 139.97 -173.22 REMARK 500 SER A 126 -159.35 -104.64 REMARK 500 ASN A 196 15.93 84.73 REMARK 500 PHE A 199 149.44 178.87 REMARK 500 LEU A 204 76.55 -115.61 REMARK 500 GLU A 209 -72.32 -45.12 REMARK 500 LEU A 213 -84.82 -84.86 REMARK 500 GLU A 215 -70.82 -70.40 REMARK 500 VAL A 216 84.85 -54.74 REMARK 500 SER A 217 39.47 -93.46 REMARK 500 ASN A 218 21.11 85.56 REMARK 500 GLN A 264 -76.97 -107.32 REMARK 500 ASN A 286 83.65 71.35 REMARK 500 SER A 289 121.43 -173.53 REMARK 500 ASN A 291 17.11 -149.22 REMARK 500 GLN A 344 55.82 -110.36 REMARK 500 LEU A 347 -50.03 -29.55 REMARK 500 SER A 377 43.30 -78.91 REMARK 500 ASP A 378 23.12 -171.39 REMARK 500 SER A 379 -166.04 -112.64 REMARK 500 GLU A 389 14.35 -61.34 REMARK 500 GLU A 390 106.43 40.74 REMARK 500 MET A 419 19.36 81.30 REMARK 500 PRO A 421 151.92 -49.56 REMARK 500 LYS A 429 11.73 -68.05 REMARK 500 CYS A 447 -155.48 68.82 REMARK 500 ILE A 448 86.40 -154.94 REMARK 500 ARG A 449 -74.64 -77.32 REMARK 500 ASN A 472 64.65 66.73 REMARK 500 ASN A 477 85.80 -46.15 REMARK 500 ASN A 485 -169.05 -101.52 REMARK 500 ALA B 95 -82.88 -57.44 REMARK 500 SER B 96 43.19 -90.41 REMARK 500 ALA B 103 15.72 -53.33 REMARK 500 LEU B 125 93.67 -65.79 REMARK 500 ASP B 127 102.18 55.00 REMARK 500 GLU B 192 129.44 -170.47 REMARK 500 SER B 202 119.06 -163.91 REMARK 500 PRO B 249 -39.66 -37.96 REMARK 500 ASN B 252 118.86 -164.90 REMARK 500 GLN B 264 -81.36 -75.35 REMARK 500 ASN B 286 81.34 78.72 REMARK 500 ASN B 291 -5.86 -59.66 REMARK 500 LEU B 339 -93.44 -60.98 REMARK 500 ILE B 340 -57.96 -15.12 REMARK 500 GLN B 363 38.20 73.16 REMARK 500 CYS B 376 -91.02 -83.67 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 90 MET A 91 144.70 REMARK 500 VAL A 114 VAL A 115 -145.06 REMARK 500 SER A 126 ASP A 127 120.18 REMARK 500 LEU A 213 GLU A 214 142.90 REMARK 500 GLU A 215 VAL A 216 133.07 REMARK 500 ASN A 218 ASN A 219 -147.60 REMARK 500 ASN A 219 CYS A 220 -147.56 REMARK 500 GLU A 224 TRP A 225 -149.82 REMARK 500 GLU A 300 LYS A 301 -146.35 REMARK 500 ASP A 378 SER A 379 147.23 REMARK 500 GLU A 390 LEU A 391 144.51 REMARK 500 LEU A 391 GLU A 392 -127.74 REMARK 500 ASN A 408 TYR A 409 -141.04 REMARK 500 GLU A 476 ASN A 477 -129.95 REMARK 500 ASN A 477 THR A 478 117.09 REMARK 500 SER B 96 MET B 97 146.47 REMARK 500 ILE B 101 SER B 102 139.08 REMARK 500 SER B 102 ALA B 103 -149.97 REMARK 500 GLU B 224 TRP B 225 -149.16 REMARK 500 ALA B 282 GLN B 283 -149.64 REMARK 500 GLU B 390 LEU B 391 -147.84 REMARK 500 LYS B 431 ARG B 432 146.80 REMARK 500 LYS B 461 ASN B 462 -142.91 REMARK 500 GLU B 475 GLU B 476 -135.01 REMARK 500 GLU B 476 ASN B 477 124.68 REMARK 500 VAL B 481 LYS B 482 -144.15 REMARK 500 VAL B 512 GLU B 513 141.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MF0 RELATED DB: PDB DBREF 3LFV A 98 518 UNP O76074 PDE5A_HUMAN 98 518 DBREF 3LFV B 98 518 UNP O76074 PDE5A_HUMAN 98 518 SEQADV 3LFV ALA A 90 UNP O76074 EXPRESSION TAG SEQADV 3LFV MET A 91 UNP O76074 EXPRESSION TAG SEQADV 3LFV GLU A 92 UNP O76074 EXPRESSION TAG SEQADV 3LFV HIS A 93 UNP O76074 EXPRESSION TAG SEQADV 3LFV MET A 94 UNP O76074 EXPRESSION TAG SEQADV 3LFV ALA A 95 UNP O76074 EXPRESSION TAG SEQADV 3LFV SER A 96 UNP O76074 EXPRESSION TAG SEQADV 3LFV MET A 97 UNP O76074 EXPRESSION TAG SEQADV 3LFV SER A 149 UNP O76074 CYS 149 ENGINEERED SEQADV 3LFV ARG A 519 UNP O76074 EXPRESSION TAG SEQADV 3LFV ASN A 520 UNP O76074 EXPRESSION TAG SEQADV 3LFV ALA B 90 UNP O76074 EXPRESSION TAG SEQADV 3LFV MET B 91 UNP O76074 EXPRESSION TAG SEQADV 3LFV GLU B 92 UNP O76074 EXPRESSION TAG SEQADV 3LFV HIS B 93 UNP O76074 EXPRESSION TAG SEQADV 3LFV MET B 94 UNP O76074 EXPRESSION TAG SEQADV 3LFV ALA B 95 UNP O76074 EXPRESSION TAG SEQADV 3LFV SER B 96 UNP O76074 EXPRESSION TAG SEQADV 3LFV MET B 97 UNP O76074 EXPRESSION TAG SEQADV 3LFV SER B 149 UNP O76074 CYS 149 ENGINEERED SEQADV 3LFV ARG B 519 UNP O76074 EXPRESSION TAG SEQADV 3LFV ASN B 520 UNP O76074 EXPRESSION TAG SEQRES 1 A 431 ALA MET GLU HIS MET ALA SER MET THR ARG LYS ILE SER SEQRES 2 A 431 ALA SER GLU PHE ASP ARG PRO LEU ARG PRO ILE VAL VAL SEQRES 3 A 431 LYS ASP SER GLU GLY THR VAL SER PHE LEU SER ASP SER SEQRES 4 A 431 GLU LYS LYS GLU GLN MET PRO LEU THR PRO PRO ARG PHE SEQRES 5 A 431 ASP HIS ASP GLU GLY ASP GLN SER SER ARG LEU LEU GLU SEQRES 6 A 431 LEU VAL LYS ASP ILE SER SER HIS LEU ASP VAL THR ALA SEQRES 7 A 431 LEU CYS HIS LYS ILE PHE LEU HIS ILE HIS GLY LEU ILE SEQRES 8 A 431 SER ALA ASP ARG TYR SER LEU PHE LEU VAL CYS GLU ASP SEQRES 9 A 431 SER SER ASN ASP LYS PHE LEU ILE SER ARG LEU PHE ASP SEQRES 10 A 431 VAL ALA GLU GLY SER THR LEU GLU GLU VAL SER ASN ASN SEQRES 11 A 431 CYS ILE ARG LEU GLU TRP ASN LYS GLY ILE VAL GLY HIS SEQRES 12 A 431 VAL ALA ALA LEU GLY GLU PRO LEU ASN ILE LYS ASP ALA SEQRES 13 A 431 TYR GLU ASP PRO ARG PHE ASN ALA GLU VAL ASP GLN ILE SEQRES 14 A 431 THR GLY TYR LYS THR GLN SER ILE LEU CYS MET PRO ILE SEQRES 15 A 431 LYS ASN HIS ARG GLU GLU VAL VAL GLY VAL ALA GLN ALA SEQRES 16 A 431 ILE ASN LYS LYS SER GLY ASN GLY GLY THR PHE THR GLU SEQRES 17 A 431 LYS ASP GLU LYS ASP PHE ALA ALA TYR LEU ALA PHE CYS SEQRES 18 A 431 GLY ILE VAL LEU HIS ASN ALA GLN LEU TYR GLU THR SER SEQRES 19 A 431 LEU LEU GLU ASN LYS ARG ASN GLN VAL LEU LEU ASP LEU SEQRES 20 A 431 ALA SER LEU ILE PHE GLU GLU GLN GLN SER LEU GLU VAL SEQRES 21 A 431 ILE LEU LYS LYS ILE ALA ALA THR ILE ILE SER PHE MET SEQRES 22 A 431 GLN VAL GLN LYS CYS THR ILE PHE ILE VAL ASP GLU ASP SEQRES 23 A 431 CYS SER ASP SER PHE SER SER VAL PHE HIS MET GLU CYS SEQRES 24 A 431 GLU GLU LEU GLU LYS SER SER ASP THR LEU THR ARG GLU SEQRES 25 A 431 HIS ASP ALA ASN LYS ILE ASN TYR MET TYR ALA GLN TYR SEQRES 26 A 431 VAL LYS ASN THR MET GLU PRO LEU ASN ILE PRO ASP VAL SEQRES 27 A 431 SER LYS ASP LYS ARG PHE PRO TRP THR THR GLU ASN THR SEQRES 28 A 431 GLY ASN VAL ASN GLN GLN CYS ILE ARG SER LEU LEU CYS SEQRES 29 A 431 THR PRO ILE LYS ASN GLY LYS LYS ASN LYS VAL ILE GLY SEQRES 30 A 431 VAL CYS GLN LEU VAL ASN LYS MET GLU GLU ASN THR GLY SEQRES 31 A 431 LYS VAL LYS PRO PHE ASN ARG ASN ASP GLU GLN PHE LEU SEQRES 32 A 431 GLU ALA PHE VAL ILE PHE CYS GLY LEU GLY ILE GLN ASN SEQRES 33 A 431 THR GLN MET TYR GLU ALA VAL GLU ARG ALA MET ALA LYS SEQRES 34 A 431 ARG ASN SEQRES 1 B 431 ALA MET GLU HIS MET ALA SER MET THR ARG LYS ILE SER SEQRES 2 B 431 ALA SER GLU PHE ASP ARG PRO LEU ARG PRO ILE VAL VAL SEQRES 3 B 431 LYS ASP SER GLU GLY THR VAL SER PHE LEU SER ASP SER SEQRES 4 B 431 GLU LYS LYS GLU GLN MET PRO LEU THR PRO PRO ARG PHE SEQRES 5 B 431 ASP HIS ASP GLU GLY ASP GLN SER SER ARG LEU LEU GLU SEQRES 6 B 431 LEU VAL LYS ASP ILE SER SER HIS LEU ASP VAL THR ALA SEQRES 7 B 431 LEU CYS HIS LYS ILE PHE LEU HIS ILE HIS GLY LEU ILE SEQRES 8 B 431 SER ALA ASP ARG TYR SER LEU PHE LEU VAL CYS GLU ASP SEQRES 9 B 431 SER SER ASN ASP LYS PHE LEU ILE SER ARG LEU PHE ASP SEQRES 10 B 431 VAL ALA GLU GLY SER THR LEU GLU GLU VAL SER ASN ASN SEQRES 11 B 431 CYS ILE ARG LEU GLU TRP ASN LYS GLY ILE VAL GLY HIS SEQRES 12 B 431 VAL ALA ALA LEU GLY GLU PRO LEU ASN ILE LYS ASP ALA SEQRES 13 B 431 TYR GLU ASP PRO ARG PHE ASN ALA GLU VAL ASP GLN ILE SEQRES 14 B 431 THR GLY TYR LYS THR GLN SER ILE LEU CYS MET PRO ILE SEQRES 15 B 431 LYS ASN HIS ARG GLU GLU VAL VAL GLY VAL ALA GLN ALA SEQRES 16 B 431 ILE ASN LYS LYS SER GLY ASN GLY GLY THR PHE THR GLU SEQRES 17 B 431 LYS ASP GLU LYS ASP PHE ALA ALA TYR LEU ALA PHE CYS SEQRES 18 B 431 GLY ILE VAL LEU HIS ASN ALA GLN LEU TYR GLU THR SER SEQRES 19 B 431 LEU LEU GLU ASN LYS ARG ASN GLN VAL LEU LEU ASP LEU SEQRES 20 B 431 ALA SER LEU ILE PHE GLU GLU GLN GLN SER LEU GLU VAL SEQRES 21 B 431 ILE LEU LYS LYS ILE ALA ALA THR ILE ILE SER PHE MET SEQRES 22 B 431 GLN VAL GLN LYS CYS THR ILE PHE ILE VAL ASP GLU ASP SEQRES 23 B 431 CYS SER ASP SER PHE SER SER VAL PHE HIS MET GLU CYS SEQRES 24 B 431 GLU GLU LEU GLU LYS SER SER ASP THR LEU THR ARG GLU SEQRES 25 B 431 HIS ASP ALA ASN LYS ILE ASN TYR MET TYR ALA GLN TYR SEQRES 26 B 431 VAL LYS ASN THR MET GLU PRO LEU ASN ILE PRO ASP VAL SEQRES 27 B 431 SER LYS ASP LYS ARG PHE PRO TRP THR THR GLU ASN THR SEQRES 28 B 431 GLY ASN VAL ASN GLN GLN CYS ILE ARG SER LEU LEU CYS SEQRES 29 B 431 THR PRO ILE LYS ASN GLY LYS LYS ASN LYS VAL ILE GLY SEQRES 30 B 431 VAL CYS GLN LEU VAL ASN LYS MET GLU GLU ASN THR GLY SEQRES 31 B 431 LYS VAL LYS PRO PHE ASN ARG ASN ASP GLU GLN PHE LEU SEQRES 32 B 431 GLU ALA PHE VAL ILE PHE CYS GLY LEU GLY ILE GLN ASN SEQRES 33 B 431 THR GLN MET TYR GLU ALA VAL GLU ARG ALA MET ALA LYS SEQRES 34 B 431 ARG ASN HELIX 1 1 MET A 91 LYS A 100 1 10 HELIX 2 2 ILE A 101 ASP A 107 5 7 HELIX 3 3 ASP A 147 SER A 161 1 15 HELIX 4 4 ASP A 164 GLY A 178 1 15 HELIX 5 5 LYS A 227 GLY A 237 1 11 HELIX 6 6 ASP A 244 ASP A 248 5 5 HELIX 7 7 ALA A 253 GLY A 260 1 8 HELIX 8 8 LYS A 298 PHE A 341 1 44 HELIX 9 9 SER A 346 GLN A 363 1 18 HELIX 10 10 TYR A 409 MET A 419 1 11 HELIX 11 11 ASN A 485 LYS A 518 1 34 HELIX 12 12 MET B 91 ALA B 95 5 5 HELIX 13 13 ASP B 147 SER B 160 1 14 HELIX 14 14 ASP B 164 GLY B 178 1 15 HELIX 15 15 LYS B 227 GLY B 237 1 11 HELIX 16 16 ASP B 244 ASP B 248 5 5 HELIX 17 17 ALA B 253 GLY B 260 1 8 HELIX 18 18 THR B 296 PHE B 341 1 46 HELIX 19 19 SER B 346 GLN B 363 1 18 HELIX 20 20 MET B 410 MET B 419 1 10 HELIX 21 21 ASN B 485 ALA B 517 1 33 SHEET 1 A 2 VAL A 115 ASP A 117 0 SHEET 2 A 2 THR A 121 SER A 123 -1 O THR A 121 N ASP A 117 SHEET 1 B 6 ILE A 221 GLU A 224 0 SHEET 2 B 6 LYS A 198 PHE A 205 -1 N SER A 202 O ILE A 221 SHEET 3 B 6 ALA A 182 GLU A 192 -1 N LEU A 189 O ILE A 201 SHEET 4 B 6 VAL A 278 LYS A 287 -1 O VAL A 281 N PHE A 188 SHEET 5 B 6 ILE A 266 LYS A 272 -1 N MET A 269 O ALA A 282 SHEET 6 B 6 LEU A 240 ILE A 242 -1 N LEU A 240 O CYS A 268 SHEET 1 C 6 LEU A 391 LYS A 393 0 SHEET 2 C 6 SER A 382 GLU A 387 -1 N HIS A 385 O LYS A 393 SHEET 3 C 6 LYS A 366 ILE A 371 -1 N CYS A 367 O MET A 386 SHEET 4 C 6 VAL A 464 VAL A 471 -1 O VAL A 467 N PHE A 370 SHEET 5 C 6 LEU A 451 LYS A 457 -1 N LEU A 452 O LEU A 470 SHEET 6 C 6 LEU A 422 ILE A 424 -1 N ILE A 424 O LEU A 451 SHEET 1 D 2 VAL B 115 LYS B 116 0 SHEET 2 D 2 VAL B 122 SER B 123 -1 O SER B 123 N VAL B 115 SHEET 1 E 6 ILE B 221 LEU B 223 0 SHEET 2 E 6 LYS B 198 PHE B 205 -1 N LEU B 200 O LEU B 223 SHEET 3 E 6 ALA B 182 GLU B 192 -1 N CYS B 191 O PHE B 199 SHEET 4 E 6 VAL B 278 LYS B 287 -1 O VAL B 281 N PHE B 188 SHEET 5 E 6 ILE B 266 LYS B 272 -1 N MET B 269 O ALA B 282 SHEET 6 E 6 LEU B 240 ILE B 242 -1 N ILE B 242 O ILE B 266 SHEET 1 F 5 SER B 382 GLU B 387 0 SHEET 2 F 5 LYS B 366 ILE B 371 -1 N ILE B 369 O PHE B 384 SHEET 3 F 5 GLY B 466 VAL B 471 -1 O VAL B 467 N PHE B 370 SHEET 4 F 5 LEU B 451 ILE B 456 -1 N THR B 454 O CYS B 468 SHEET 5 F 5 LEU B 422 ILE B 424 -1 N ILE B 424 O LEU B 451 CRYST1 144.189 144.189 134.867 90.00 90.00 120.00 P 31 2 1 12 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 0.006935 0.004004 0.000000 0.00000 SCALE2 0.000000 0.008008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007415 0.00000