HEADER HYDROLASE/HYDROLASE INHIBITOR 09-JUL-13 4LM2 TITLE CRYSTAL STRUCTURE OF PDE10A2 WITH FRAGMENT ZT462 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE COMPND 3 10A; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 439-779; COMPND 6 EC: 3.1.4.17, 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: PDE10A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS FRAGMENT SCREENING, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.SRIDHAR,J.BADGER,C.LOGAN,B.CHIE-LEON,V.NIENABER REVDAT 3 20-SEP-23 4LM2 1 REMARK SEQADV LINK REVDAT 2 26-MAR-14 4LM2 1 JRNL REVDAT 1 26-FEB-14 4LM2 0 JRNL AUTH M.I.RECHT,V.SRIDHAR,J.BADGER,P.Y.BOUNAUD,C.LOGAN, JRNL AUTH 2 B.CHIE-LEON,V.NIENABER,F.E.TORRES JRNL TITL IDENTIFICATION AND OPTIMIZATION OF PDE10A INHIBITORS USING JRNL TITL 2 FRAGMENT-BASED SCREENING BY NANOCALORIMETRY AND X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF J BIOMOL SCREEN V. 19 497 2014 JRNL REFN ISSN 1087-0571 JRNL PMID 24375910 JRNL DOI 10.1177/1087057113516493 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 88932 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4693 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4903 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE SET COUNT : 251 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5235 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -0.18000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.593 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 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): 5442 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7374 ; 1.484 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 655 ; 5.265 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 250 ;35.668 ;23.960 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 957 ;13.106 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.729 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 817 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4078 ; 0.008 ; 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): 3278 ; 1.183 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5318 ; 1.844 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2164 ; 2.388 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2056 ; 3.650 ; 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: NULL REMARK 4 REMARK 4 4LM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-11 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.55700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2OUR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 4450, 0.2M CALCIUM ACETATE, REMARK 280 50MM BME, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 26.09200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.56500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.19150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.56500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.09200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.19150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 GLY A 445 REMARK 465 SER A 776 REMARK 465 SER A 777 REMARK 465 PRO A 778 REMARK 465 SER A 779 REMARK 465 VAL A 780 REMARK 465 ALA A 781 REMARK 465 GLN A 782 REMARK 465 LYS A 783 REMARK 465 ALA A 784 REMARK 465 ALA A 785 REMARK 465 ALA A 786 REMARK 465 SER A 787 REMARK 465 GLU A 788 REMARK 465 ASP A 789 REMARK 465 GLY B 445 REMARK 465 ALA B 446 REMARK 465 GLY B 447 REMARK 465 ILE B 775 REMARK 465 SER B 776 REMARK 465 SER B 777 REMARK 465 PRO B 778 REMARK 465 SER B 779 REMARK 465 VAL B 780 REMARK 465 ALA B 781 REMARK 465 GLN B 782 REMARK 465 LYS B 783 REMARK 465 ALA B 784 REMARK 465 ALA B 785 REMARK 465 ALA B 786 REMARK 465 SER B 787 REMARK 465 GLU B 788 REMARK 465 ASP B 789 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 SER A 453 OG REMARK 470 GLU A 454 CG CD OE1 OE2 REMARK 470 GLN A 461 CG CD OE1 NE2 REMARK 470 LYS A 470 CG CD CE NZ REMARK 470 GLU A 506 CG CD OE1 OE2 REMARK 470 ARG A 521 NE CZ NH1 NH2 REMARK 470 LYS A 577 CD CE NZ REMARK 470 GLU A 606 CG CD OE1 OE2 REMARK 470 GLU A 647 CG CD OE1 OE2 REMARK 470 LYS A 753 CD CE NZ REMARK 470 THR A 773 OG1 CG2 REMARK 470 ILE A 775 CG1 CG2 CD1 REMARK 470 GLU B 454 CG CD OE1 OE2 REMARK 470 LYS B 470 CG CD CE NZ REMARK 470 GLU B 504 CG CD OE1 OE2 REMARK 470 ARG B 521 CD NE CZ NH1 NH2 REMARK 470 SER B 573 OG REMARK 470 LYS B 577 CG CD CE NZ REMARK 470 GLU B 606 CG CD OE1 OE2 REMARK 470 SER B 617 OG REMARK 470 GLU B 647 CG CD OE1 OE2 REMARK 470 ARG B 767 NE CZ NH1 NH2 REMARK 470 TRP B 774 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 774 CZ3 CH2 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 496 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 674 CB - CG - OD2 ANGL. DEV. = 9.6 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 TYR A 524 -50.09 -126.95 REMARK 500 VAL A 733 -63.45 -122.35 REMARK 500 TYR B 524 -41.18 -130.57 REMARK 500 VAL B 733 -57.20 -123.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE FOUR DIVALENT CATIONS ARE REPRESENTED BY NI BUT THIS REMARK 600 IDENTIFICATION IS SPECULATIVE 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 NI A 901 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 529 NE2 REMARK 620 2 HIS A 563 NE2 93.8 REMARK 620 3 ASP A 564 OD2 89.2 87.1 REMARK 620 4 ASP A 674 OD2 86.4 89.2 174.0 REMARK 620 5 HOH A1014 O 86.8 176.6 96.3 87.5 REMARK 620 6 HOH A1171 O 164.5 100.8 96.8 88.5 78.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 902 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 564 OD1 REMARK 620 2 HOH A1067 O 161.4 REMARK 620 3 HOH A1169 O 110.4 85.6 REMARK 620 4 HOH A1170 O 83.9 88.1 86.2 REMARK 620 5 HOH A1171 O 97.3 92.4 88.0 174.1 REMARK 620 6 HOH A1172 O 84.3 79.3 164.9 92.2 93.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 901 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 529 NE2 REMARK 620 2 HIS B 563 NE2 93.2 REMARK 620 3 ASP B 564 OD2 89.6 86.8 REMARK 620 4 ASP B 674 OD1 82.4 94.7 171.9 REMARK 620 5 HOH B1134 O 82.7 170.9 85.0 92.8 REMARK 620 6 HOH B1135 O 166.3 99.0 97.3 90.4 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 902 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 564 OD1 REMARK 620 2 HOH B1034 O 157.3 REMARK 620 3 HOH B1075 O 85.1 82.9 REMARK 620 4 HOH B1076 O 79.5 80.5 85.8 REMARK 620 5 HOH B1133 O 102.0 95.6 82.9 168.5 REMARK 620 6 HOH B1135 O 96.4 94.2 175.4 90.2 101.0 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 8ZE A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LKQ RELATED DB: PDB REMARK 900 RELATED ID: 4LLJ RELATED DB: PDB REMARK 900 RELATED ID: 4LLL RELATED DB: PDB REMARK 900 RELATED ID: 4LLP RELATED DB: PDB REMARK 900 RELATED ID: 4LLX RELATED DB: PDB REMARK 900 RELATED ID: 4LM0 RELATED DB: PDB REMARK 900 RELATED ID: 4LM1 RELATED DB: PDB REMARK 900 RELATED ID: 4LM3 RELATED DB: PDB REMARK 900 RELATED ID: 4LM4 RELATED DB: PDB DBREF 4LM2 A 449 789 UNP Q9Y233 PDE10_HUMAN 439 779 DBREF 4LM2 B 449 789 UNP Q9Y233 PDE10_HUMAN 439 779 SEQADV 4LM2 GLY A 445 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 ALA A 446 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 GLY A 447 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 THR A 448 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 GLY B 445 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 ALA B 446 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 GLY B 447 UNP Q9Y233 EXPRESSION TAG SEQADV 4LM2 THR B 448 UNP Q9Y233 EXPRESSION TAG SEQRES 1 A 345 GLY ALA GLY THR SER ILE CYS THR SER GLU GLU TRP GLN SEQRES 2 A 345 GLY LEU MET GLN PHE THR LEU PRO VAL ARG LEU CYS LYS SEQRES 3 A 345 GLU ILE GLU LEU PHE HIS PHE ASP ILE GLY PRO PHE GLU SEQRES 4 A 345 ASN MET TRP PRO GLY ILE PHE VAL TYR MET VAL HIS ARG SEQRES 5 A 345 SER CYS GLY THR SER CYS PHE GLU LEU GLU LYS LEU CYS SEQRES 6 A 345 ARG PHE ILE MET SER VAL LYS LYS ASN TYR ARG ARG VAL SEQRES 7 A 345 PRO TYR HIS ASN TRP LYS HIS ALA VAL THR VAL ALA HIS SEQRES 8 A 345 CYS MET TYR ALA ILE LEU GLN ASN ASN HIS THR LEU PHE SEQRES 9 A 345 THR ASP LEU GLU ARG LYS GLY LEU LEU ILE ALA CYS LEU SEQRES 10 A 345 CYS HIS ASP LEU ASP HIS ARG GLY PHE SER ASN SER TYR SEQRES 11 A 345 LEU GLN LYS PHE ASP HIS PRO LEU ALA ALA LEU TYR SER SEQRES 12 A 345 THR SER THR MET GLU GLN HIS HIS PHE SER GLN THR VAL SEQRES 13 A 345 SER ILE LEU GLN LEU GLU GLY HIS ASN ILE PHE SER THR SEQRES 14 A 345 LEU SER SER SER GLU TYR GLU GLN VAL LEU GLU ILE ILE SEQRES 15 A 345 ARG LYS ALA ILE ILE ALA THR ASP LEU ALA LEU TYR PHE SEQRES 16 A 345 GLY ASN ARG LYS GLN LEU GLU GLU MET TYR GLN THR GLY SEQRES 17 A 345 SER LEU ASN LEU ASN ASN GLN SER HIS ARG ASP ARG VAL SEQRES 18 A 345 ILE GLY LEU MET MET THR ALA CYS ASP LEU CYS SER VAL SEQRES 19 A 345 THR LYS LEU TRP PRO VAL THR LYS LEU THR ALA ASN ASP SEQRES 20 A 345 ILE TYR ALA GLU PHE TRP ALA GLU GLY ASP GLU MET LYS SEQRES 21 A 345 LYS LEU GLY ILE GLN PRO ILE PRO MET MET ASP ARG ASP SEQRES 22 A 345 LYS LYS ASP GLU VAL PRO GLN GLY GLN LEU GLY PHE TYR SEQRES 23 A 345 ASN ALA VAL ALA ILE PRO CYS TYR THR THR LEU THR GLN SEQRES 24 A 345 ILE LEU PRO PRO THR GLU PRO LEU LEU LYS ALA CYS ARG SEQRES 25 A 345 ASP ASN LEU SER GLN TRP GLU LYS VAL ILE ARG GLY GLU SEQRES 26 A 345 GLU THR ALA THR TRP ILE SER SER PRO SER VAL ALA GLN SEQRES 27 A 345 LYS ALA ALA ALA SER GLU ASP SEQRES 1 B 345 GLY ALA GLY THR SER ILE CYS THR SER GLU GLU TRP GLN SEQRES 2 B 345 GLY LEU MET GLN PHE THR LEU PRO VAL ARG LEU CYS LYS SEQRES 3 B 345 GLU ILE GLU LEU PHE HIS PHE ASP ILE GLY PRO PHE GLU SEQRES 4 B 345 ASN MET TRP PRO GLY ILE PHE VAL TYR MET VAL HIS ARG SEQRES 5 B 345 SER CYS GLY THR SER CYS PHE GLU LEU GLU LYS LEU CYS SEQRES 6 B 345 ARG PHE ILE MET SER VAL LYS LYS ASN TYR ARG ARG VAL SEQRES 7 B 345 PRO TYR HIS ASN TRP LYS HIS ALA VAL THR VAL ALA HIS SEQRES 8 B 345 CYS MET TYR ALA ILE LEU GLN ASN ASN HIS THR LEU PHE SEQRES 9 B 345 THR ASP LEU GLU ARG LYS GLY LEU LEU ILE ALA CYS LEU SEQRES 10 B 345 CYS HIS ASP LEU ASP HIS ARG GLY PHE SER ASN SER TYR SEQRES 11 B 345 LEU GLN LYS PHE ASP HIS PRO LEU ALA ALA LEU TYR SER SEQRES 12 B 345 THR SER THR MET GLU GLN HIS HIS PHE SER GLN THR VAL SEQRES 13 B 345 SER ILE LEU GLN LEU GLU GLY HIS ASN ILE PHE SER THR SEQRES 14 B 345 LEU SER SER SER GLU TYR GLU GLN VAL LEU GLU ILE ILE SEQRES 15 B 345 ARG LYS ALA ILE ILE ALA THR ASP LEU ALA LEU TYR PHE SEQRES 16 B 345 GLY ASN ARG LYS GLN LEU GLU GLU MET TYR GLN THR GLY SEQRES 17 B 345 SER LEU ASN LEU ASN ASN GLN SER HIS ARG ASP ARG VAL SEQRES 18 B 345 ILE GLY LEU MET MET THR ALA CYS ASP LEU CYS SER VAL SEQRES 19 B 345 THR LYS LEU TRP PRO VAL THR LYS LEU THR ALA ASN ASP SEQRES 20 B 345 ILE TYR ALA GLU PHE TRP ALA GLU GLY ASP GLU MET LYS SEQRES 21 B 345 LYS LEU GLY ILE GLN PRO ILE PRO MET MET ASP ARG ASP SEQRES 22 B 345 LYS LYS ASP GLU VAL PRO GLN GLY GLN LEU GLY PHE TYR SEQRES 23 B 345 ASN ALA VAL ALA ILE PRO CYS TYR THR THR LEU THR GLN SEQRES 24 B 345 ILE LEU PRO PRO THR GLU PRO LEU LEU LYS ALA CYS ARG SEQRES 25 B 345 ASP ASN LEU SER GLN TRP GLU LYS VAL ILE ARG GLY GLU SEQRES 26 B 345 GLU THR ALA THR TRP ILE SER SER PRO SER VAL ALA GLN SEQRES 27 B 345 LYS ALA ALA ALA SER GLU ASP HET 8ZE A 900 12 HET NI A 901 1 HET NI A 902 1 HET NI B 901 1 HET NI B 902 1 HETNAM 8ZE 2,3-DIHYDRO-1,4-BENZODIOXIN-6-YLMETHANOL HETNAM NI NICKEL (II) ION FORMUL 3 8ZE C9 H10 O3 FORMUL 4 NI 4(NI 2+) FORMUL 8 HOH *390(H2 O) HELIX 1 1 THR A 452 PHE A 462 1 11 HELIX 2 2 PRO A 465 GLU A 473 1 9 HELIX 3 3 ILE A 479 ASN A 484 5 6 HELIX 4 4 MET A 485 GLY A 499 1 15 HELIX 5 5 GLU A 504 ASN A 518 1 15 HELIX 6 6 ASN A 526 ASN A 544 1 19 HELIX 7 7 HIS A 545 PHE A 548 5 4 HELIX 8 8 THR A 549 HIS A 563 1 15 HELIX 9 9 SER A 571 PHE A 578 1 8 HELIX 10 10 HIS A 580 TYR A 586 1 7 HELIX 11 11 SER A 589 GLN A 604 1 16 HELIX 12 12 SER A 615 THR A 633 1 19 HELIX 13 13 ASP A 634 THR A 651 1 18 HELIX 14 14 ASN A 658 LEU A 675 1 18 HELIX 15 15 CYS A 676 LYS A 680 5 5 HELIX 16 16 LEU A 681 LEU A 706 1 26 HELIX 17 17 ILE A 711 ASP A 720 5 10 HELIX 18 18 GLU A 721 VAL A 733 1 13 HELIX 19 19 VAL A 733 LEU A 745 1 13 HELIX 20 20 THR A 748 ARG A 767 1 20 HELIX 21 21 THR B 452 GLN B 461 1 10 HELIX 22 22 ARG B 467 ILE B 472 1 6 HELIX 23 23 ILE B 479 ASN B 484 5 6 HELIX 24 24 MET B 485 GLY B 499 1 15 HELIX 25 25 GLU B 504 ASN B 518 1 15 HELIX 26 26 ASN B 526 ASN B 544 1 19 HELIX 27 27 HIS B 545 PHE B 548 5 4 HELIX 28 28 THR B 549 HIS B 563 1 15 HELIX 29 29 SER B 571 PHE B 578 1 8 HELIX 30 30 HIS B 580 TYR B 586 1 7 HELIX 31 31 SER B 589 GLN B 604 1 16 HELIX 32 32 SER B 615 THR B 633 1 19 HELIX 33 33 ASP B 634 THR B 651 1 18 HELIX 34 34 ASN B 658 LEU B 675 1 18 HELIX 35 35 CYS B 676 LYS B 680 5 5 HELIX 36 36 LEU B 681 LYS B 686 1 6 HELIX 37 37 LEU B 687 ALA B 689 5 3 HELIX 38 38 ASN B 690 ILE B 692 5 3 HELIX 39 39 TYR B 693 LYS B 705 1 13 HELIX 40 40 ILE B 711 ASP B 715 5 5 HELIX 41 41 GLU B 721 VAL B 733 1 13 HELIX 42 42 VAL B 733 LEU B 745 1 13 HELIX 43 43 THR B 748 ARG B 767 1 20 LINK NE2 HIS A 529 NI NI A 901 1555 1555 2.17 LINK NE2 HIS A 563 NI NI A 901 1555 1555 2.20 LINK OD2 ASP A 564 NI NI A 901 1555 1555 1.95 LINK OD1 ASP A 564 NI NI A 902 1555 1555 2.20 LINK OD2 ASP A 674 NI NI A 901 1555 1555 1.95 LINK NI NI A 901 O HOH A1014 1555 1555 2.50 LINK NI NI A 901 O HOH A1171 1555 1555 2.04 LINK NI NI A 902 O HOH A1067 1555 1555 2.25 LINK NI NI A 902 O HOH A1169 1555 1555 2.27 LINK NI NI A 902 O HOH A1170 1555 1555 2.20 LINK NI NI A 902 O HOH A1171 1555 1555 2.18 LINK NI NI A 902 O HOH A1172 1555 1555 2.21 LINK NE2 HIS B 529 NI NI B 901 1555 1555 2.24 LINK NE2 HIS B 563 NI NI B 901 1555 1555 2.18 LINK OD2 ASP B 564 NI NI B 901 1555 1555 2.41 LINK OD1 ASP B 564 NI NI B 902 1555 1555 2.34 LINK OD1 ASP B 674 NI NI B 901 1555 1555 2.17 LINK NI NI B 901 O HOH B1134 1555 1555 2.16 LINK NI NI B 901 O HOH B1135 1555 1555 2.14 LINK NI NI B 902 O HOH B1034 1555 1555 2.33 LINK NI NI B 902 O HOH B1075 1555 1555 2.22 LINK NI NI B 902 O HOH B1076 1555 1555 2.24 LINK NI NI B 902 O HOH B1133 1555 1555 2.28 LINK NI NI B 902 O HOH B1135 1555 1555 1.99 SITE 1 AC1 8 TYR A 524 SER A 677 VAL A 678 ILE A 692 SITE 2 AC1 8 PHE A 696 GLN A 726 PHE A 729 HOH A1007 SITE 1 AC2 6 HIS A 529 HIS A 563 ASP A 564 ASP A 674 SITE 2 AC2 6 HOH A1014 HOH A1171 SITE 1 AC3 6 ASP A 564 HOH A1067 HOH A1169 HOH A1170 SITE 2 AC3 6 HOH A1171 HOH A1172 SITE 1 AC4 7 HIS B 529 HIS B 563 ASP B 564 ASP B 674 SITE 2 AC4 7 NI B 902 HOH B1134 HOH B1135 SITE 1 AC5 7 ASP B 564 NI B 901 HOH B1034 HOH B1075 SITE 2 AC5 7 HOH B1076 HOH B1133 HOH B1135 CRYST1 52.184 82.383 155.130 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006446 0.00000