PDB Short entry for 4Y2P HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 10-FEB-15 4Y2P TITLE STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE IN COMPLEX WITH N-METHYL-1-[3- TITLE 2 (PYRIDIN-3-YL)PHENYL]METHANAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL EPOXIDE HYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-555; COMPND 5 EC: 3.3.2.10; COMPND 6 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: EPHX2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR COMPLEX, HYDROLASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.AMANO,T.YAMAGUCHI REVDAT 3 20-MAR-24 4Y2P 1 REMARK REVDAT 2 05-FEB-20 4Y2P 1 SOURCE JRNL REMARK REVDAT 1 06-MAY-15 4Y2P 0 JRNL AUTH Y.AMANO,E.TANABE,T.YAMAGUCHI JRNL TITL IDENTIFICATION OF N-ETHYLMETHYLAMINE AS A NOVEL SCAFFOLD FOR JRNL TITL 2 INHIBITORS OF SOLUBLE EPOXIDE HYDROLASE BY CRYSTALLOGRAPHIC JRNL TITL 3 FRAGMENT SCREENING JRNL REF BIOORG.MED.CHEM. V. 23 2310 2015 JRNL REFN ESSN 1464-3391 JRNL PMID 25862210 JRNL DOI 10.1016/J.BMC.2015.03.083 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 37865 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2765 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4323 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.190 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.195 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4448 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6026 ; 2.199 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 545 ; 6.978 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;34.615 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 783 ;18.333 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;22.383 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 659 ; 0.156 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3369 ; 0.012 ; 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): 2183 ; 2.863 ; 2.854 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2727 ; 3.773 ; 4.265 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2262 ; 4.450 ; 3.244 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6931 ; 9.570 ;24.310 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 : 1.20 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 4Y2P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39866 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 80.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM PHOSPHATE, AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE, PEG3350, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 163.10133 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 81.55067 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 122.32600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.77533 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 203.87667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 163.10133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 81.55067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.77533 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 122.32600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 203.87667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -93.05900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 122.32600 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 1 REMARK 465 ASN A 548 REMARK 465 PRO A 549 REMARK 465 PRO A 550 REMARK 465 VAL A 551 REMARK 465 VAL A 552 REMARK 465 SER A 553 REMARK 465 LYS A 554 REMARK 465 MET A 555 REMARK 465 HIS A 556 REMARK 465 HIS A 557 REMARK 465 HIS A 558 REMARK 465 HIS A 559 REMARK 465 HIS A 560 REMARK 465 HIS A 561 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 69 OE1 GLU A 69 7465 2.12 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 99 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 113 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 7.5 DEGREES REMARK 500 LEU A 183 CA - CB - CG ANGL. DEV. = 19.4 DEGREES REMARK 500 LEU A 183 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 PRO A 225 C - N - CA ANGL. DEV. = -9.4 DEGREES REMARK 500 ARG A 287 CB - CG - CD ANGL. DEV. = 17.7 DEGREES REMARK 500 ARG A 287 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 287 NE - CZ - NH1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 287 NE - CZ - NH2 ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 353 CG - CD - NE ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG A 353 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 LEU A 438 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 471 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 471 NE - CZ - NH2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 482 CD - NE - CZ ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 482 NE - CZ - NH1 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG A 482 NE - CZ - NH2 ANGL. DEV. = 10.1 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 LEU A 10 -72.99 -90.86 REMARK 500 VAL A 13 -71.50 -126.48 REMARK 500 GLN A 204 -96.83 -102.62 REMARK 500 GLU A 269 -139.08 -117.03 REMARK 500 ASP A 335 -128.56 64.09 REMARK 500 ASN A 359 -48.86 81.72 REMARK 500 MET A 419 34.28 -89.02 REMARK 500 LEU A 514 130.00 -39.18 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 MET A 291 ASP A 292 143.11 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD2 REMARK 620 2 ASP A 11 O 86.7 REMARK 620 3 ASP A 185 OD1 114.2 85.3 REMARK 620 N 1 2 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3C5 A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y2J RELATED DB: PDB REMARK 900 RELATED ID: 4Y2Q RELATED DB: PDB REMARK 900 RELATED ID: 4Y2R RELATED DB: PDB REMARK 900 RELATED ID: 4Y2S RELATED DB: PDB REMARK 900 RELATED ID: 4Y2T RELATED DB: PDB REMARK 900 RELATED ID: 4Y2U RELATED DB: PDB REMARK 900 RELATED ID: 4Y2V RELATED DB: PDB REMARK 900 RELATED ID: 4Y2X RELATED DB: PDB REMARK 900 RELATED ID: 4Y2Y RELATED DB: PDB DBREF 4Y2P A 1 555 UNP P34913 HYES_HUMAN 1 555 SEQADV 4Y2P HIS A 556 UNP P34913 EXPRESSION TAG SEQADV 4Y2P HIS A 557 UNP P34913 EXPRESSION TAG SEQADV 4Y2P HIS A 558 UNP P34913 EXPRESSION TAG SEQADV 4Y2P HIS A 559 UNP P34913 EXPRESSION TAG SEQADV 4Y2P HIS A 560 UNP P34913 EXPRESSION TAG SEQADV 4Y2P HIS A 561 UNP P34913 EXPRESSION TAG SEQRES 1 A 561 MET THR LEU ARG ALA ALA VAL PHE ASP LEU ASP GLY VAL SEQRES 2 A 561 LEU ALA LEU PRO ALA VAL PHE GLY VAL LEU GLY ARG THR SEQRES 3 A 561 GLU GLU ALA LEU ALA LEU PRO ARG GLY LEU LEU ASN ASP SEQRES 4 A 561 ALA PHE GLN LYS GLY GLY PRO GLU GLY ALA THR THR ARG SEQRES 5 A 561 LEU MET LYS GLY GLU ILE THR LEU SER GLN TRP ILE PRO SEQRES 6 A 561 LEU MET GLU GLU ASN CYS ARG LYS CYS SER GLU THR ALA SEQRES 7 A 561 LYS VAL CYS LEU PRO LYS ASN PHE SER ILE LYS GLU ILE SEQRES 8 A 561 PHE ASP LYS ALA ILE SER ALA ARG LYS ILE ASN ARG PRO SEQRES 9 A 561 MET LEU GLN ALA ALA LEU MET LEU ARG LYS LYS GLY PHE SEQRES 10 A 561 THR THR ALA ILE LEU THR ASN THR TRP LEU ASP ASP ARG SEQRES 11 A 561 ALA GLU ARG ASP GLY LEU ALA GLN LEU MET CYS GLU LEU SEQRES 12 A 561 LYS MET HIS PHE ASP PHE LEU ILE GLU SER CYS GLN VAL SEQRES 13 A 561 GLY MET VAL LYS PRO GLU PRO GLN ILE TYR LYS PHE LEU SEQRES 14 A 561 LEU ASP THR LEU LYS ALA SER PRO SER GLU VAL VAL PHE SEQRES 15 A 561 LEU ASP ASP ILE GLY ALA ASN LEU LYS PRO ALA ARG ASP SEQRES 16 A 561 LEU GLY MET VAL THR ILE LEU VAL GLN ASP THR ASP THR SEQRES 17 A 561 ALA LEU LYS GLU LEU GLU LYS VAL THR GLY ILE GLN LEU SEQRES 18 A 561 LEU ASN THR PRO ALA PRO LEU PRO THR SER CYS ASN PRO SEQRES 19 A 561 SER ASP MET SER HIS GLY TYR VAL THR VAL LYS PRO ARG SEQRES 20 A 561 VAL ARG LEU HIS PHE VAL GLU LEU GLY SER GLY PRO ALA SEQRES 21 A 561 VAL CYS LEU CYS HIS GLY PHE PRO GLU SER TRP TYR SER SEQRES 22 A 561 TRP ARG TYR GLN ILE PRO ALA LEU ALA GLN ALA GLY TYR SEQRES 23 A 561 ARG VAL LEU ALA MET ASP MET LYS GLY TYR GLY GLU SER SEQRES 24 A 561 SER ALA PRO PRO GLU ILE GLU GLU TYR CYS MET GLU VAL SEQRES 25 A 561 LEU CYS LYS GLU MET VAL THR PHE LEU ASP LYS LEU GLY SEQRES 26 A 561 LEU SER GLN ALA VAL PHE ILE GLY HIS ASP TRP GLY GLY SEQRES 27 A 561 MET LEU VAL TRP TYR MET ALA LEU PHE TYR PRO GLU ARG SEQRES 28 A 561 VAL ARG ALA VAL ALA SER LEU ASN THR PRO PHE ILE PRO SEQRES 29 A 561 ALA ASN PRO ASN MET SER PRO LEU GLU SER ILE LYS ALA SEQRES 30 A 561 ASN PRO VAL PHE ASP TYR GLN LEU TYR PHE GLN GLU PRO SEQRES 31 A 561 GLY VAL ALA GLU ALA GLU LEU GLU GLN ASN LEU SER ARG SEQRES 32 A 561 THR PHE LYS SER LEU PHE ARG ALA SER ASP GLU SER VAL SEQRES 33 A 561 LEU SER MET HIS LYS VAL CYS GLU ALA GLY GLY LEU PHE SEQRES 34 A 561 VAL ASN SER PRO GLU GLU PRO SER LEU SER ARG MET VAL SEQRES 35 A 561 THR GLU GLU GLU ILE GLN PHE TYR VAL GLN GLN PHE LYS SEQRES 36 A 561 LYS SER GLY PHE ARG GLY PRO LEU ASN TRP TYR ARG ASN SEQRES 37 A 561 MET GLU ARG ASN TRP LYS TRP ALA CYS LYS SER LEU GLY SEQRES 38 A 561 ARG LYS ILE LEU ILE PRO ALA LEU MET VAL THR ALA GLU SEQRES 39 A 561 LYS ASP PHE VAL LEU VAL PRO GLN MET SER GLN HIS MET SEQRES 40 A 561 GLU ASP TRP ILE PRO HIS LEU LYS ARG GLY HIS ILE GLU SEQRES 41 A 561 ASP CYS GLY HIS TRP THR GLN MET ASP LYS PRO THR GLU SEQRES 42 A 561 VAL ASN GLN ILE LEU ILE LYS TRP LEU ASP SER ASP ALA SEQRES 43 A 561 ARG ASN PRO PRO VAL VAL SER LYS MET HIS HIS HIS HIS SEQRES 44 A 561 HIS HIS HET MG A 601 1 HET 3C5 A 602 15 HETNAM MG MAGNESIUM ION HETNAM 3C5 N-METHYL-1-[3-(PYRIDIN-3-YL)PHENYL]METHANAMINE FORMUL 2 MG MG 2+ FORMUL 3 3C5 C13 H14 N2 FORMUL 4 HOH *119(H2 O) HELIX 1 AA1 ALA A 18 PHE A 20 5 3 HELIX 2 AA2 GLY A 21 ALA A 31 1 11 HELIX 3 AA3 GLY A 35 LYS A 43 1 9 HELIX 4 AA4 GLY A 44 GLU A 47 5 4 HELIX 5 AA5 GLY A 48 LYS A 55 1 8 HELIX 6 AA6 THR A 59 ALA A 78 1 20 HELIX 7 AA7 SER A 87 ARG A 99 1 13 HELIX 8 AA8 ASN A 102 LYS A 115 1 14 HELIX 9 AA9 GLU A 132 MET A 145 1 14 HELIX 10 AB1 SER A 153 GLY A 157 1 5 HELIX 11 AB2 GLU A 162 LYS A 174 1 13 HELIX 12 AB3 SER A 176 SER A 178 5 3 HELIX 13 AB4 ILE A 186 LEU A 196 1 11 HELIX 14 AB5 ASP A 205 GLY A 218 1 14 HELIX 15 AB6 ASN A 233 MET A 237 5 5 HELIX 16 AB7 SER A 270 ARG A 275 5 6 HELIX 17 AB8 TYR A 276 ALA A 284 1 9 HELIX 18 AB9 GLU A 304 TYR A 308 5 5 HELIX 19 AC1 CYS A 309 GLY A 325 1 17 HELIX 20 AC2 ASP A 335 TYR A 348 1 14 HELIX 21 AC3 SER A 370 ALA A 377 1 8 HELIX 22 AC4 ASN A 378 VAL A 380 5 3 HELIX 23 AC5 PHE A 381 PHE A 387 1 7 HELIX 24 AC6 GLY A 391 ASN A 400 1 10 HELIX 25 AC7 ASN A 400 PHE A 409 1 10 HELIX 26 AC8 ALA A 411 SER A 415 5 5 HELIX 27 AC9 LYS A 421 GLY A 426 1 6 HELIX 28 AD1 THR A 443 GLY A 458 1 16 HELIX 29 AD2 PHE A 459 TRP A 465 1 7 HELIX 30 AD3 ASN A 468 LYS A 478 1 11 HELIX 31 AD4 VAL A 500 GLN A 505 5 6 HELIX 32 AD5 HIS A 506 TRP A 510 5 5 HELIX 33 AD6 TRP A 525 LYS A 530 1 6 HELIX 34 AD7 LYS A 530 ALA A 546 1 17 SHEET 1 AA1 5 PHE A 149 GLU A 152 0 SHEET 2 AA1 5 THR A 118 THR A 123 1 N ILE A 121 O ILE A 151 SHEET 3 AA1 5 ALA A 5 PHE A 8 1 N PHE A 8 O ALA A 120 SHEET 4 AA1 5 VAL A 180 ASP A 184 1 O VAL A 181 N VAL A 7 SHEET 5 AA1 5 VAL A 199 LEU A 202 1 O ILE A 201 N PHE A 182 SHEET 1 AA2 2 ALA A 15 LEU A 16 0 SHEET 2 AA2 2 LYS A 100 ILE A 101 -1 O LYS A 100 N LEU A 16 SHEET 1 AA3 8 SER A 238 LYS A 245 0 SHEET 2 AA3 8 VAL A 248 LEU A 255 -1 O LEU A 250 N VAL A 242 SHEET 3 AA3 8 ARG A 287 MET A 291 -1 O VAL A 288 N LEU A 255 SHEET 4 AA3 8 ALA A 260 CYS A 264 1 N VAL A 261 O LEU A 289 SHEET 5 AA3 8 ALA A 329 HIS A 334 1 O VAL A 330 N CYS A 262 SHEET 6 AA3 8 VAL A 352 LEU A 358 1 O ALA A 356 N GLY A 333 SHEET 7 AA3 8 ALA A 488 ALA A 493 1 O VAL A 491 N SER A 357 SHEET 8 AA3 8 LYS A 515 ILE A 519 1 O LYS A 515 N ALA A 488 LINK OD2 ASP A 9 MG MG A 601 1555 1555 2.61 LINK O ASP A 11 MG MG A 601 1555 1555 2.83 LINK OD1 ASP A 185 MG MG A 601 1555 1555 2.45 CISPEP 1 LEU A 16 PRO A 17 0 -9.80 CISPEP 2 LYS A 160 PRO A 161 0 0.37 CISPEP 3 PHE A 267 PRO A 268 0 -8.55 SITE 1 AC1 4 ASP A 9 ASP A 11 ASP A 185 ILE A 186 SITE 1 AC2 5 PHE A 267 ASP A 335 TYR A 383 TYR A 466 SITE 2 AC2 5 HOH A 771 CRYST1 93.059 93.059 244.652 90.00 90.00 120.00 P 65 2 2 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 0.010746 0.006204 0.000000 0.00000 SCALE2 0.000000 0.012408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004087 0.00000