PDB Short entry for 4L2X HEADER TRANSFERASE/TRANSFERASE INHIBITOR 04-JUN-13 4L2X TITLE CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH MAGNESIUM, CL02134, TITLE 2 AND INORGANIC PYROPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESYL PYROPHOSPHATE SYNTHASE; COMPND 3 CHAIN: F; COMPND 4 FRAGMENT: UNP RESIDUES 67-419; COMPND 5 EC: 2.5.1.10, 2.5.1.1; 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: FDPS, FPS, KIAA1293; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.PARK,C.-Y.LEUNG,Y.S.TSANTRIZOS,A.M.BERGHUIS REVDAT 3 20-SEP-23 4L2X 1 REMARK SEQADV LINK REVDAT 2 15-JAN-14 4L2X 1 JRNL REVDAT 1 01-JAN-14 4L2X 0 JRNL AUTH C.Y.LEUNG,J.PARK,J.W.DE SCHUTTER,M.SEBAG,A.M.BERGHUIS, JRNL AUTH 2 Y.S.TSANTRIZOS JRNL TITL THIENOPYRIMIDINE BISPHOSPHONATE (THPBP) INHIBITORS OF THE JRNL TITL 2 HUMAN FARNESYL PYROPHOSPHATE SYNTHASE: OPTIMIZATION AND JRNL TITL 3 CHARACTERIZATION OF THE MODE OF INHIBITION. JRNL REF J.MED.CHEM. V. 56 7939 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23998921 JRNL DOI 10.1021/JM400946F REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 13394 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 704 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 842 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2687 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.17000 REMARK 3 B22 (A**2) : -6.17000 REMARK 3 B33 (A**2) : 12.35000 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): 0.560 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.265 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.554 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2784 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2562 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3795 ; 1.697 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5858 ; 0.851 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 6.180 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;37.461 ;24.640 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 439 ;15.073 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.066 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 423 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3183 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 642 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4L2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : ACCEL/BRUKER DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14376 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 9.480 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.52 REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.7.0032 REMARK 200 STARTING MODEL: PDB ENTRY 4H5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG8000, 20% GLYCEROL, 0.16 M REMARK 280 MAGNESIUM ACETATE, 0.08 M SODIUM CACODYLATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.38500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.67000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.19250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.67000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.67000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.57750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.67000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.67000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.19250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.67000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.67000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.57750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 34.38500 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: 5250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 F -21 REMARK 465 GLY F -20 REMARK 465 SER F -19 REMARK 465 SER F -18 REMARK 465 HIS F -17 REMARK 465 HIS F -16 REMARK 465 HIS F -15 REMARK 465 HIS F -14 REMARK 465 HIS F -13 REMARK 465 HIS F -12 REMARK 465 SER F -11 REMARK 465 SER F -10 REMARK 465 GLY F -9 REMARK 465 ARG F -8 REMARK 465 GLU F -7 REMARK 465 ASN F -6 REMARK 465 LEU F -5 REMARK 465 TYR F -4 REMARK 465 PHE F -3 REMARK 465 GLN F -2 REMARK 465 GLY F -1 REMARK 465 HIS F 0 REMARK 465 MET F 1 REMARK 465 ASN F 2 REMARK 465 GLY F 3 REMARK 465 ASP F 4 REMARK 465 GLN F 5 REMARK 465 ASN F 6 REMARK 465 SER F 7 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 ASP F 8 CG OD1 OD2 REMARK 470 VAL F 9 CG1 CG2 REMARK 470 GLN F 12 CG CD OE1 NE2 REMARK 470 GLN F 15 CG CD OE1 NE2 REMARK 470 GLN F 23 CG CD OE1 NE2 REMARK 470 ARG F 26 CG CD NE CZ NH1 NH2 REMARK 470 GLU F 30 CD OE1 OE2 REMARK 470 MET F 33 CG SD CE REMARK 470 GLU F 73 CD OE1 OE2 REMARK 470 ARG F 75 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 76 CD CE NZ REMARK 470 LEU F 82 CG CD1 CD2 REMARK 470 LYS F 121 CE NZ REMARK 470 LYS F 144 CD CE NZ REMARK 470 ARG F 148 NE CZ NH1 NH2 REMARK 470 GLU F 149 CD OE1 OE2 REMARK 470 VAL F 183 CG1 CG2 REMARK 470 VAL F 186 CG1 CG2 REMARK 470 LYS F 191 NZ REMARK 470 LYS F 194 CE NZ REMARK 470 GLU F 222 CG CD OE1 OE2 REMARK 470 LYS F 223 CG CD CE NZ REMARK 470 LYS F 230 NZ REMARK 470 SER F 253 OG REMARK 470 GLU F 281 CG CD OE1 OE2 REMARK 470 GLU F 288 CD OE1 OE2 REMARK 470 LYS F 293 CG CD CE NZ REMARK 470 GLU F 296 CG CD OE1 OE2 REMARK 470 ASP F 309 CG OD1 OD2 REMARK 470 ARG F 346 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 347 CE NZ REMARK 470 TYR F 349 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS F 350 CG CD CE NZ REMARK 470 ARG F 352 CG CD NE CZ NH1 NH2 REMARK 470 LYS F 353 CD CE NZ 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 PRO F 74 -18.36 -48.66 REMARK 500 VAL F 124 -62.73 -123.93 REMARK 500 PHE F 206 -59.52 -121.83 REMARK 500 THR F 260 -5.95 -157.00 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 F 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 103 OD1 REMARK 620 2 ASP F 107 OD2 82.9 REMARK 620 3 YL2 F 401 OAV 73.2 79.2 REMARK 620 4 YL2 F 401 OAZ 81.3 154.0 76.5 REMARK 620 5 HOH F 507 O 158.7 104.6 88.5 84.0 REMARK 620 6 HOH F 508 O 84.5 111.1 154.4 87.8 110.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 103 OD2 REMARK 620 2 ASP F 107 OD2 86.0 REMARK 620 3 YL2 F 401 OAV 95.0 82.5 REMARK 620 4 HOH F 501 O 84.2 170.2 98.8 REMARK 620 5 HOH F 502 O 84.0 97.2 179.0 81.4 REMARK 620 6 HOH F 503 O 156.2 110.5 103.9 78.7 77.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 243 OD2 REMARK 620 2 YL2 F 401 OAY 114.2 REMARK 620 3 YL2 F 401 OAW 100.4 97.2 REMARK 620 4 HOH F 504 O 96.0 87.5 159.2 REMARK 620 5 HOH F 505 O 79.5 163.7 88.5 82.0 REMARK 620 6 HOH F 506 O 154.2 90.2 84.0 75.8 75.1 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 YL2 F 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP F 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JVJ RELATED DB: PDB DBREF 4L2X F 1 353 UNP P14324 FPPS_HUMAN 67 419 SEQADV 4L2X MET F -21 UNP P14324 EXPRESSION TAG SEQADV 4L2X GLY F -20 UNP P14324 EXPRESSION TAG SEQADV 4L2X SER F -19 UNP P14324 EXPRESSION TAG SEQADV 4L2X SER F -18 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F -17 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F -16 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F -15 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F -14 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F -13 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F -12 UNP P14324 EXPRESSION TAG SEQADV 4L2X SER F -11 UNP P14324 EXPRESSION TAG SEQADV 4L2X SER F -10 UNP P14324 EXPRESSION TAG SEQADV 4L2X GLY F -9 UNP P14324 EXPRESSION TAG SEQADV 4L2X ARG F -8 UNP P14324 EXPRESSION TAG SEQADV 4L2X GLU F -7 UNP P14324 EXPRESSION TAG SEQADV 4L2X ASN F -6 UNP P14324 EXPRESSION TAG SEQADV 4L2X LEU F -5 UNP P14324 EXPRESSION TAG SEQADV 4L2X TYR F -4 UNP P14324 EXPRESSION TAG SEQADV 4L2X PHE F -3 UNP P14324 EXPRESSION TAG SEQADV 4L2X GLN F -2 UNP P14324 EXPRESSION TAG SEQADV 4L2X GLY F -1 UNP P14324 EXPRESSION TAG SEQADV 4L2X HIS F 0 UNP P14324 EXPRESSION TAG SEQRES 1 F 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 F 375 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET ASN GLY ASP SEQRES 3 F 375 GLN ASN SER ASP VAL TYR ALA GLN GLU LYS GLN ASP PHE SEQRES 4 F 375 VAL GLN HIS PHE SER GLN ILE VAL ARG VAL LEU THR GLU SEQRES 5 F 375 ASP GLU MET GLY HIS PRO GLU ILE GLY ASP ALA ILE ALA SEQRES 6 F 375 ARG LEU LYS GLU VAL LEU GLU TYR ASN ALA ILE GLY GLY SEQRES 7 F 375 LYS TYR ASN ARG GLY LEU THR VAL VAL VAL ALA PHE ARG SEQRES 8 F 375 GLU LEU VAL GLU PRO ARG LYS GLN ASP ALA ASP SER LEU SEQRES 9 F 375 GLN ARG ALA TRP THR VAL GLY TRP CYS VAL GLU LEU LEU SEQRES 10 F 375 GLN ALA PHE PHE LEU VAL ALA ASP ASP ILE MET ASP SER SEQRES 11 F 375 SER LEU THR ARG ARG GLY GLN ILE CYS TRP TYR GLN LYS SEQRES 12 F 375 PRO GLY VAL GLY LEU ASP ALA ILE ASN ASP ALA ASN LEU SEQRES 13 F 375 LEU GLU ALA CYS ILE TYR ARG LEU LEU LYS LEU TYR CYS SEQRES 14 F 375 ARG GLU GLN PRO TYR TYR LEU ASN LEU ILE GLU LEU PHE SEQRES 15 F 375 LEU GLN SER SER TYR GLN THR GLU ILE GLY GLN THR LEU SEQRES 16 F 375 ASP LEU LEU THR ALA PRO GLN GLY ASN VAL ASP LEU VAL SEQRES 17 F 375 ARG PHE THR GLU LYS ARG TYR LYS SER ILE VAL LYS TYR SEQRES 18 F 375 LYS THR ALA PHE TYR SER PHE TYR LEU PRO ILE ALA ALA SEQRES 19 F 375 ALA MET TYR MET ALA GLY ILE ASP GLY GLU LYS GLU HIS SEQRES 20 F 375 ALA ASN ALA LYS LYS ILE LEU LEU GLU MET GLY GLU PHE SEQRES 21 F 375 PHE GLN ILE GLN ASP ASP TYR LEU ASP LEU PHE GLY ASP SEQRES 22 F 375 PRO SER VAL THR GLY LYS ILE GLY THR ASP ILE GLN ASP SEQRES 23 F 375 ASN LYS CYS SER TRP LEU VAL VAL GLN CYS LEU GLN ARG SEQRES 24 F 375 ALA THR PRO GLU GLN TYR GLN ILE LEU LYS GLU ASN TYR SEQRES 25 F 375 GLY GLN LYS GLU ALA GLU LYS VAL ALA ARG VAL LYS ALA SEQRES 26 F 375 LEU TYR GLU GLU LEU ASP LEU PRO ALA VAL PHE LEU GLN SEQRES 27 F 375 TYR GLU GLU ASP SER TYR SER HIS ILE MET ALA LEU ILE SEQRES 28 F 375 GLU GLN TYR ALA ALA PRO LEU PRO PRO ALA VAL PHE LEU SEQRES 29 F 375 GLY LEU ALA ARG LYS ILE TYR LYS ARG ARG LYS HET YL2 F 401 28 HET POP F 402 9 HET MG F 403 1 HET MG F 404 1 HET MG F 405 1 HETNAM YL2 ({[6-(4-CYCLOPROPYLPHENYL)THIENO[2,3-D]PYRIMIDIN-4- HETNAM 2 YL2 YL]AMINO}METHANEDIYL)BIS(PHOSPHONIC ACID) HETNAM POP PYROPHOSPHATE 2- HETNAM MG MAGNESIUM ION FORMUL 2 YL2 C16 H17 N3 O6 P2 S FORMUL 3 POP H2 O7 P2 2- FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *15(H2 O) HELIX 1 1 ASP F 8 THR F 29 1 22 HELIX 2 2 HIS F 35 GLU F 37 5 3 HELIX 3 3 ILE F 38 ALA F 53 1 16 HELIX 4 4 TYR F 58 GLU F 70 1 13 HELIX 5 5 ASP F 78 SER F 108 1 31 HELIX 6 6 TRP F 118 LYS F 121 5 4 HELIX 7 7 VAL F 124 LEU F 126 5 3 HELIX 8 8 ASP F 127 ARG F 148 1 22 HELIX 9 9 TYR F 152 THR F 177 1 26 HELIX 10 10 THR F 189 THR F 201 1 13 HELIX 11 11 THR F 201 PHE F 206 1 6 HELIX 12 12 PHE F 206 ALA F 217 1 12 HELIX 13 13 GLY F 221 GLY F 250 1 30 HELIX 14 14 ASP F 251 GLY F 256 1 6 HELIX 15 15 SER F 268 ALA F 278 1 11 HELIX 16 16 THR F 279 TYR F 290 1 12 HELIX 17 17 GLU F 294 LEU F 308 1 15 HELIX 18 18 ASP F 309 ALA F 333 1 25 HELIX 19 19 PRO F 337 TYR F 349 1 13 SHEET 1 A 2 THR F 111 ARG F 112 0 SHEET 2 A 2 GLN F 115 ILE F 116 -1 O GLN F 115 N ARG F 112 LINK OD1 ASP F 103 MG MG F 403 1555 1555 2.06 LINK OD2 ASP F 103 MG MG F 404 1555 1555 2.03 LINK OD2 ASP F 107 MG MG F 403 1555 1555 2.06 LINK OD2 ASP F 107 MG MG F 404 1555 1555 2.08 LINK OD2 ASP F 243 MG MG F 405 1555 1555 2.24 LINK OAV YL2 F 401 MG MG F 403 1555 1555 2.27 LINK OAZ YL2 F 401 MG MG F 403 1555 1555 2.30 LINK OAV YL2 F 401 MG MG F 404 1555 1555 2.11 LINK OAY YL2 F 401 MG MG F 405 1555 1555 1.73 LINK OAW YL2 F 401 MG MG F 405 1555 1555 2.09 LINK MG MG F 403 O HOH F 507 1555 1555 1.95 LINK MG MG F 403 O HOH F 508 1555 1555 2.25 LINK MG MG F 404 O HOH F 501 1555 1555 1.91 LINK MG MG F 404 O HOH F 502 1555 1555 2.24 LINK MG MG F 404 O HOH F 503 1555 1555 2.17 LINK MG MG F 405 O HOH F 504 1555 1555 2.15 LINK MG MG F 405 O HOH F 505 1555 1555 2.10 LINK MG MG F 405 O HOH F 506 1555 1555 2.30 CISPEP 1 ALA F 334 PRO F 335 0 6.89 SITE 1 AC1 22 PHE F 99 ASP F 103 ASP F 107 ARG F 112 SITE 2 AC1 22 ASN F 130 THR F 167 GLU F 168 GLN F 171 SITE 3 AC1 22 LYS F 200 THR F 201 GLN F 240 ASP F 243 SITE 4 AC1 22 LYS F 257 MG F 403 MG F 404 MG F 405 SITE 5 AC1 22 HOH F 501 HOH F 504 HOH F 505 HOH F 506 SITE 6 AC1 22 HOH F 507 HOH F 513 SITE 1 AC2 8 GLY F 56 LYS F 57 ARG F 60 GLN F 96 SITE 2 AC2 8 ARG F 113 PHE F 239 HOH F 509 HOH F 510 SITE 1 AC3 6 ASP F 103 ASP F 107 YL2 F 401 MG F 404 SITE 2 AC3 6 HOH F 507 HOH F 508 SITE 1 AC4 8 ASP F 103 ASP F 107 ASP F 174 YL2 F 401 SITE 2 AC4 8 MG F 403 HOH F 501 HOH F 502 HOH F 503 SITE 1 AC5 5 ASP F 243 YL2 F 401 HOH F 504 HOH F 505 SITE 2 AC5 5 HOH F 506 CRYST1 111.340 111.340 68.770 90.00 90.00 90.00 P 41 21 2 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 0.008981 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008981 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014541 0.00000