HEADER LIGASE 07-APR-25 9UDM TITLE COCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC PHENYLALANYL-TRNA SYNTHETASE TITLE 2 AND AN INHIBITOR IN THE PRESENCE OF ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHENYLALANINE--TRNA LIGASE ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CML33,PHENYLALANYL-TRNA SYNTHETASE ALPHA SUBUNIT,PHERS; COMPND 5 EC: 6.1.1.20; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PHENYLALANINE--TRNA LIGASE BETA SUBUNIT; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: PHENYLALANYL-TRNA SYNTHETASE BETA SUBUNIT,PHERS; COMPND 11 EC: 6.1.1.20; COMPND 12 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: FARSA, FARS, FARSL, FARSLA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: FARSB, FARSLB, FRSB, HSPC173; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRNA LIGASE, INHIBITOR, COMPLEX, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR H.QIAO,Z.HEI,P.FANG REVDAT 1 15-APR-26 9UDM 0 JRNL AUTH H.QIAO,Z.HEI,P.FANG JRNL TITL COCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC PHENYLALANYL-TRNA JRNL TITL 2 SYNTHETASE AND AN INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25043 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.2600 - 8.0100 0.98 1784 154 0.1786 0.1965 REMARK 3 2 8.0100 - 6.3700 1.00 1696 147 0.2151 0.2596 REMARK 3 3 6.3600 - 5.5600 1.00 1687 146 0.2335 0.2994 REMARK 3 4 5.5600 - 5.0500 1.00 1655 144 0.2016 0.2087 REMARK 3 5 5.0500 - 4.6900 1.00 1634 142 0.1844 0.2392 REMARK 3 6 4.6900 - 4.4200 1.00 1648 142 0.1829 0.2006 REMARK 3 7 4.4200 - 4.2000 1.00 1620 141 0.1878 0.2315 REMARK 3 8 4.2000 - 4.0100 1.00 1620 141 0.2366 0.2689 REMARK 3 9 4.0100 - 3.8600 1.00 1633 141 0.2497 0.3047 REMARK 3 10 3.8600 - 3.7300 1.00 1609 140 0.2760 0.3205 REMARK 3 11 3.7300 - 3.6100 1.00 1627 141 0.2918 0.3915 REMARK 3 12 3.6100 - 3.5100 1.00 1605 139 0.3339 0.3211 REMARK 3 13 3.5100 - 3.4100 1.00 1617 141 0.3703 0.4388 REMARK 3 14 3.4100 - 3.3300 1.00 1610 139 0.3660 0.4278 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 NULL REMARK 3 ANGLE : 1.415 NULL REMARK 3 CHIRALITY : 0.078 1097 REMARK 3 PLANARITY : 0.020 1247 REMARK 3 DIHEDRAL : 7.416 965 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 34.0935 -40.4696 18.6453 REMARK 3 T TENSOR REMARK 3 T11: 0.9507 T22: 1.0177 REMARK 3 T33: 0.9299 T12: -0.0390 REMARK 3 T13: -0.0168 T23: -0.1787 REMARK 3 L TENSOR REMARK 3 L11: 1.5548 L22: 0.2909 REMARK 3 L33: 0.9171 L12: -0.2577 REMARK 3 L13: -1.2251 L23: 0.1261 REMARK 3 S TENSOR REMARK 3 S11: -0.1287 S12: 0.1852 S13: -0.2058 REMARK 3 S21: -0.0474 S22: -0.0518 S23: 0.0620 REMARK 3 S31: 0.1110 S32: -0.2066 S33: 0.1730 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9UDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 10-APR-25. REMARK 100 THE DEPOSITION ID IS D_1300058297. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25133 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.330 REMARK 200 RESOLUTION RANGE LOW (A) : 48.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.89000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3L4G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM FORMATE, 0.05 M TRIS PH REMARK 280 8.5, 8% V/V PEG 500 MME AND 8% W/V PEG 20000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 139.91850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.95200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.95200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 209.87775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.95200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.95200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.95925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.95200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.95200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 209.87775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.95200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.95200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.95925 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 139.91850 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 66230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 107.90400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -107.90400 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 A 177 REMARK 465 GLY A 178 REMARK 465 SER A 179 REMARK 465 SER A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 LYS A 187 REMARK 465 GLN A 188 REMARK 465 MET B 1 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 GLU A 195 CG CD OE1 OE2 REMARK 470 ASP A 204 CG OD1 OD2 REMARK 470 ARG A 205 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 ASP A 249 CG OD1 OD2 REMARK 470 ARG A 271 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 GLN A 287 CG CD OE1 NE2 REMARK 470 ARG A 295 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 297 CG CD CE NZ REMARK 470 ARG A 298 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 302 CG CD OE1 NE2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 LYS A 315 CG CD CE NZ REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 LYS A 343 CG CD CE NZ REMARK 470 LYS A 349 CG CD CE NZ REMARK 470 LEU A 362 CG CD1 CD2 REMARK 470 ASP A 363 CG OD1 OD2 REMARK 470 LYS A 397 CG CD CE NZ REMARK 470 GLU A 414 CG CD OE1 OE2 REMARK 470 LYS A 427 CG CD CE NZ REMARK 470 LYS A 428 CG CD CE NZ REMARK 470 LYS A 481 CG CD CE NZ REMARK 470 LYS B 7 CG CD CE NZ REMARK 470 GLU B 22 CG CD OE1 OE2 REMARK 470 GLU B 26 CG CD OE1 OE2 REMARK 470 LYS B 42 CG CD CE NZ REMARK 470 GLU B 43 CG CD OE1 OE2 REMARK 470 LYS B 47 CG CD CE NZ REMARK 470 GLU B 48 CG CD OE1 OE2 REMARK 470 GLN B 49 CG CD OE1 NE2 REMARK 470 LYS B 53 CG CD CE NZ REMARK 470 VAL B 61 CG1 CG2 REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 LYS B 92 CG CD CE NZ REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 LYS B 116 CG CD CE NZ REMARK 470 LYS B 130 CG CD CE NZ REMARK 470 GLN B 148 CG CD OE1 NE2 REMARK 470 LYS B 153 CG CD CE NZ REMARK 470 ARG B 177 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 184 CG CD CE NZ REMARK 470 LYS B 190 CG CD CE NZ REMARK 470 LYS B 202 CG CD CE NZ REMARK 470 HIS B 212 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 243 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 249 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 279 CG CD OE1 OE2 REMARK 470 LYS B 295 CG CD CE NZ REMARK 470 LYS B 306 CG CD CE NZ REMARK 470 MET B 308 CG SD CE REMARK 470 LYS B 316 CG CD CE NZ REMARK 470 ARG B 321 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 325 CG CD OE1 OE2 REMARK 470 LYS B 329 CG CD CE NZ REMARK 470 LYS B 337 CG CD CE NZ REMARK 470 GLN B 378 CG CD OE1 NE2 REMARK 470 LYS B 383 CG CD CE NZ REMARK 470 THR B 410 OG1 CG2 REMARK 470 LYS B 426 CG CD CE NZ REMARK 470 LYS B 435 CG CD CE NZ REMARK 470 LYS B 443 CG CD CE NZ REMARK 470 LYS B 473 CG CD CE NZ REMARK 470 LYS B 483 CG CD CE NZ REMARK 470 LYS B 492 CG CD CE NZ REMARK 470 LYS B 504 CG CD CE NZ REMARK 470 LYS B 530 CG CD CE NZ REMARK 470 LYS B 536 CG CD CE NZ REMARK 470 GLU B 539 CG CD OE1 OE2 REMARK 470 LYS B 560 CG CD CE NZ REMARK 470 LYS B 571 CG CD CE NZ 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 OG1 THR A 361 O ASP A 363 1.92 REMARK 500 N ARG B 8 O VAL B 61 2.15 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 ILE A 373 CG1 - CB - CG2 ANGL. DEV. = -18.1 DEGREES REMARK 500 LEU A 443 CB - CG - CD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 LEU B 156 CB - CG - CD2 ANGL. DEV. = -13.7 DEGREES REMARK 500 LEU B 393 CB - CG - CD2 ANGL. DEV. = -13.6 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 LYS A 208 62.44 -161.23 REMARK 500 PRO A 269 2.98 -69.67 REMARK 500 SER A 301 -62.08 -91.66 REMARK 500 GLU A 360 -140.77 52.37 REMARK 500 HIS A 366 -123.07 42.48 REMARK 500 VAL B 60 -8.21 -59.93 REMARK 500 ASN B 149 -76.98 -115.09 REMARK 500 ARG B 154 -9.07 72.63 REMARK 500 ASP B 165 0.58 -64.55 REMARK 500 PRO B 185 -177.26 -68.74 REMARK 500 LEU B 211 -66.71 -96.61 REMARK 500 ASN B 216 51.99 -118.38 REMARK 500 ASP B 225 -169.69 -102.62 REMARK 500 ASN B 441 70.18 40.17 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 B 233 PRO B 234 -141.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 358 0.10 SIDE CHAIN REMARK 500 ARG B 98 0.15 SIDE CHAIN REMARK 500 ARG B 305 0.18 SIDE CHAIN REMARK 500 ARG B 495 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9UDL RELATED DB: PDB DBREF 9UDM A 187 490 UNP Q9Y285 SYFA_HUMAN 187 490 DBREF 9UDM B 1 589 UNP Q9NSD9 SYFB_HUMAN 1 589 SEQADV 9UDM MET A 177 UNP Q9Y285 INITIATING METHIONINE SEQADV 9UDM GLY A 178 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM SER A 179 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM SER A 180 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM HIS A 181 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM HIS A 182 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM HIS A 183 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM HIS A 184 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM HIS A 185 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM HIS A 186 UNP Q9Y285 EXPRESSION TAG SEQADV 9UDM ILE B 585 UNP Q9NSD9 VAL 585 VARIANT SEQRES 1 A 314 MET GLY SER SER HIS HIS HIS HIS HIS HIS LYS GLN GLU SEQRES 2 A 314 THR GLU LEU SER PRO GLU MET ILE SER SER GLY SER TRP SEQRES 3 A 314 ARG ASP ARG PRO PHE LYS PRO TYR ASN PHE LEU ALA HIS SEQRES 4 A 314 GLY VAL LEU PRO ASP SER GLY HIS LEU HIS PRO LEU LEU SEQRES 5 A 314 LYS VAL ARG SER GLN PHE ARG GLN ILE PHE LEU GLU MET SEQRES 6 A 314 GLY PHE THR GLU MET PRO THR ASP ASN PHE ILE GLU SER SEQRES 7 A 314 SER PHE TRP ASN PHE ASP ALA LEU PHE GLN PRO GLN GLN SEQRES 8 A 314 HIS PRO ALA ARG ASP GLN HIS ASP THR PHE PHE LEU ARG SEQRES 9 A 314 ASP PRO ALA GLU ALA LEU GLN LEU PRO MET ASP TYR VAL SEQRES 10 A 314 GLN ARG VAL LYS ARG THR HIS SER GLN GLY GLY TYR GLY SEQRES 11 A 314 SER GLN GLY TYR LYS TYR ASN TRP LYS LEU ASP GLU ALA SEQRES 12 A 314 ARG LYS ASN LEU LEU ARG THR HIS THR THR SER ALA SER SEQRES 13 A 314 ALA ARG ALA LEU TYR ARG LEU ALA GLN LYS LYS PRO PHE SEQRES 14 A 314 THR PRO VAL LYS TYR PHE SER ILE ASP ARG VAL PHE ARG SEQRES 15 A 314 ASN GLU THR LEU ASP ALA THR HIS LEU ALA GLU PHE HIS SEQRES 16 A 314 GLN ILE GLU GLY VAL VAL ALA ASP HIS GLY LEU THR LEU SEQRES 17 A 314 GLY HIS LEU MET GLY VAL LEU ARG GLU PHE PHE THR LYS SEQRES 18 A 314 LEU GLY ILE THR GLN LEU ARG PHE LYS PRO ALA TYR ASN SEQRES 19 A 314 PRO TYR THR GLU PRO SER MET GLU VAL PHE SER TYR HIS SEQRES 20 A 314 GLN GLY LEU LYS LYS TRP VAL GLU VAL GLY ASN SER GLY SEQRES 21 A 314 VAL PHE ARG PRO GLU MET LEU LEU PRO MET GLY LEU PRO SEQRES 22 A 314 GLU ASN VAL SER VAL ILE ALA TRP GLY LEU SER LEU GLU SEQRES 23 A 314 ARG PRO THR MET ILE LYS TYR GLY ILE ASN ASN ILE ARG SEQRES 24 A 314 GLU LEU VAL GLY HIS LYS VAL ASN LEU GLN MET VAL TYR SEQRES 25 A 314 ASP SER SEQRES 1 B 589 MET PRO THR VAL SER VAL LYS ARG ASP LEU LEU PHE GLN SEQRES 2 B 589 ALA LEU GLY ARG THR TYR THR ASP GLU GLU PHE ASP GLU SEQRES 3 B 589 LEU CYS PHE GLU PHE GLY LEU GLU LEU ASP GLU ILE THR SEQRES 4 B 589 SER GLU LYS GLU ILE ILE SER LYS GLU GLN GLY ASN VAL SEQRES 5 B 589 LYS ALA ALA GLY ALA SER ASP VAL VAL LEU TYR LYS ILE SEQRES 6 B 589 ASP VAL PRO ALA ASN ARG TYR ASP LEU LEU CYS LEU GLU SEQRES 7 B 589 GLY LEU VAL ARG GLY LEU GLN VAL PHE LYS GLU ARG ILE SEQRES 8 B 589 LYS ALA PRO VAL TYR LYS ARG VAL MET PRO ASP GLY LYS SEQRES 9 B 589 ILE GLN LYS LEU ILE ILE THR GLU GLU THR ALA LYS ILE SEQRES 10 B 589 ARG PRO PHE ALA VAL ALA ALA VAL LEU ARG ASN ILE LYS SEQRES 11 B 589 PHE THR LYS ASP ARG TYR ASP SER PHE ILE GLU LEU GLN SEQRES 12 B 589 GLU LYS LEU HIS GLN ASN ILE CYS ARG LYS ARG ALA LEU SEQRES 13 B 589 VAL ALA ILE GLY THR HIS ASP LEU ASP THR LEU SER GLY SEQRES 14 B 589 PRO PHE THR TYR THR ALA LYS ARG PRO SER ASP ILE LYS SEQRES 15 B 589 PHE LYS PRO LEU ASN LYS THR LYS GLU TYR THR ALA CYS SEQRES 16 B 589 GLU LEU MET ASN ILE TYR LYS THR ASP ASN HIS LEU LYS SEQRES 17 B 589 HIS TYR LEU HIS ILE ILE GLU ASN LYS PRO LEU TYR PRO SEQRES 18 B 589 VAL ILE TYR ASP SER ASN GLY VAL VAL LEU SER MET PRO SEQRES 19 B 589 PRO ILE ILE ASN GLY ASP HIS SER ARG ILE THR VAL ASN SEQRES 20 B 589 THR ARG ASN ILE PHE ILE GLU CYS THR GLY THR ASP PHE SEQRES 21 B 589 THR LYS ALA LYS ILE VAL LEU ASP ILE ILE VAL THR MET SEQRES 22 B 589 PHE SER GLU TYR CYS GLU ASN GLN PHE THR VAL GLU ALA SEQRES 23 B 589 ALA GLU VAL VAL PHE PRO ASN GLY LYS SER HIS THR PHE SEQRES 24 B 589 PRO GLU LEU ALA TYR ARG LYS GLU MET VAL ARG ALA ASP SEQRES 25 B 589 LEU ILE ASN LYS LYS VAL GLY ILE ARG GLU THR PRO GLU SEQRES 26 B 589 ASN LEU ALA LYS LEU LEU THR ARG MET TYR LEU LYS SER SEQRES 27 B 589 GLU VAL ILE GLY ASP GLY ASN GLN ILE GLU ILE GLU ILE SEQRES 28 B 589 PRO PRO THR ARG ALA ASP ILE ILE HIS ALA CYS ASP ILE SEQRES 29 B 589 VAL GLU ASP ALA ALA ILE ALA TYR GLY TYR ASN ASN ILE SEQRES 30 B 589 GLN MET THR LEU PRO LYS THR TYR THR ILE ALA ASN GLN SEQRES 31 B 589 PHE PRO LEU ASN LYS LEU THR GLU LEU LEU ARG HIS ASP SEQRES 32 B 589 MET ALA ALA ALA GLY PHE THR GLU ALA LEU THR PHE ALA SEQRES 33 B 589 LEU CYS SER GLN GLU ASP ILE ALA ASP LYS LEU GLY VAL SEQRES 34 B 589 ASP ILE SER ALA THR LYS ALA VAL HIS ILE SER ASN PRO SEQRES 35 B 589 LYS THR ALA GLU PHE GLN VAL ALA ARG THR THR LEU LEU SEQRES 36 B 589 PRO GLY LEU LEU LYS THR ILE ALA ALA ASN ARG LYS MET SEQRES 37 B 589 PRO LEU PRO LEU LYS LEU PHE GLU ILE SER ASP ILE VAL SEQRES 38 B 589 ILE LYS ASP SER ASN THR ASP VAL GLY ALA LYS ASN TYR SEQRES 39 B 589 ARG HIS LEU CYS ALA VAL TYR TYR ASN LYS ASN PRO GLY SEQRES 40 B 589 PHE GLU ILE ILE HIS GLY LEU LEU ASP ARG ILE MET GLN SEQRES 41 B 589 LEU LEU ASP VAL PRO PRO GLY GLU ASP LYS GLY GLY TYR SEQRES 42 B 589 VAL ILE LYS ALA SER GLU GLY PRO ALA PHE PHE PRO GLY SEQRES 43 B 589 ARG CYS ALA GLU ILE PHE ALA ARG GLY GLN SER VAL GLY SEQRES 44 B 589 LYS LEU GLY VAL LEU HIS PRO ASP VAL ILE THR LYS PHE SEQRES 45 B 589 GLU LEU THR MET PRO CYS SER SER LEU GLU ILE ASN ILE SEQRES 46 B 589 GLY PRO PHE LEU HET LCF A 501 27 HETNAM LCF [6-(4-CHLOROPHENYL)-2,2-DIMETHYL-7-PHENYL-2,3-DIHYDRO- HETNAM 2 LCF 1H-PYRROLIZIN-5-YL]ACETIC ACID HETSYN LCF LICOFELONE FORMUL 3 LCF C23 H22 CL N O2 HELIX 1 AA1 SER A 193 GLY A 200 1 8 HELIX 2 AA2 HIS A 225 GLU A 240 1 16 HELIX 3 AA3 SER A 255 PHE A 259 1 5 HELIX 4 AA4 ASP A 260 PHE A 263 5 4 HELIX 5 AA5 HIS A 268 ASP A 272 5 5 HELIX 6 AA6 PRO A 289 GLN A 302 1 14 HELIX 7 AA7 LYS A 315 LYS A 321 1 7 HELIX 8 AA8 THR A 328 GLN A 341 1 14 HELIX 9 AA9 THR A 383 GLY A 399 1 17 HELIX 10 AB1 ARG A 439 LEU A 444 1 6 HELIX 11 AB2 PRO A 445 GLY A 447 5 3 HELIX 12 AB3 LEU A 461 GLY A 470 1 10 HELIX 13 AB4 ASN A 473 LEU A 477 5 5 HELIX 14 AB5 ASN A 483 SER A 490 1 8 HELIX 15 AB6 ARG B 8 GLY B 16 1 9 HELIX 16 AB7 THR B 20 GLY B 32 1 13 HELIX 17 AB8 SER B 40 LYS B 47 1 8 HELIX 18 AB9 CYS B 76 LYS B 88 1 13 HELIX 19 AC1 GLU B 113 ARG B 118 1 6 HELIX 20 AC2 THR B 132 ASN B 149 1 18 HELIX 21 AC3 ASP B 165 LEU B 167 5 3 HELIX 22 AC4 ARG B 177 ASP B 180 5 4 HELIX 23 AC5 ALA B 194 THR B 203 1 10 HELIX 24 AC6 LEU B 207 ASN B 216 1 10 HELIX 25 AC7 ASP B 259 SER B 275 1 17 HELIX 26 AC8 GLU B 276 CYS B 278 5 3 HELIX 27 AC9 ALA B 311 GLY B 319 1 9 HELIX 28 AD1 THR B 323 MET B 334 1 12 HELIX 29 AD2 HIS B 360 GLY B 373 1 14 HELIX 30 AD3 TYR B 374 ILE B 377 5 4 HELIX 31 AD4 PHE B 391 GLY B 408 1 18 HELIX 32 AD5 SER B 419 ALA B 424 1 6 HELIX 33 AD6 ASP B 430 LYS B 435 1 6 HELIX 34 AD7 THR B 444 GLN B 448 5 5 HELIX 35 AD8 LEU B 454 ASN B 465 1 12 HELIX 36 AD9 GLY B 507 LEU B 522 1 16 HELIX 37 AE1 GLY B 527 GLY B 531 5 5 HELIX 38 AE2 HIS B 565 PHE B 572 1 8 HELIX 39 AE3 GLY B 586 LEU B 589 5 4 SHEET 1 AA1 7 THR A 244 GLU A 245 0 SHEET 2 AA1 7 VAL A 348 PHE A 357 1 O LYS A 349 N THR A 244 SHEET 3 AA1 7 GLU A 369 HIS A 380 -1 O GLN A 372 N ASP A 354 SHEET 4 AA1 7 VAL A 452 SER A 460 -1 O LEU A 459 N ILE A 373 SHEET 5 AA1 7 LYS A 428 PHE A 438 -1 N ASN A 434 O GLY A 458 SHEET 6 AA1 7 THR A 413 HIS A 423 -1 N VAL A 419 O GLY A 433 SHEET 7 AA1 7 ARG A 404 PRO A 407 -1 N ARG A 404 O PHE A 420 SHEET 1 AA2 3 ILE A 252 SER A 254 0 SHEET 2 AA2 3 ASN A 322 LEU A 324 -1 O LEU A 323 N GLU A 253 SHEET 3 AA2 3 PHE A 277 PHE A 278 -1 N PHE A 277 O LEU A 324 SHEET 1 AA3 3 THR B 3 LYS B 7 0 SHEET 2 AA3 3 LEU B 62 ASP B 66 -1 O ILE B 65 N VAL B 4 SHEET 3 AA3 3 GLU B 34 ILE B 38 -1 N GLU B 34 O ASP B 66 SHEET 1 AA4 2 LYS B 97 VAL B 99 0 SHEET 2 AA4 2 THR B 283 GLU B 285 1 O VAL B 284 N VAL B 99 SHEET 1 AA5 7 ILE B 237 ASN B 238 0 SHEET 2 AA5 7 VAL B 230 MET B 233 -1 N MET B 233 O ILE B 237 SHEET 3 AA5 7 TYR B 220 TYR B 224 -1 N ILE B 223 O LEU B 231 SHEET 4 AA5 7 PHE B 171 LYS B 176 -1 N LYS B 176 O TYR B 220 SHEET 5 AA5 7 LYS B 107 ILE B 110 1 N ILE B 109 O TYR B 173 SHEET 6 AA5 7 ALA B 287 VAL B 290 1 O VAL B 290 N LEU B 108 SHEET 7 AA5 7 SER B 296 PHE B 299 -1 O PHE B 299 N ALA B 287 SHEET 1 AA6 3 PHE B 120 ARG B 127 0 SHEET 2 AA6 3 ASN B 250 GLY B 257 -1 O ILE B 253 N ALA B 124 SHEET 3 AA6 3 VAL B 157 ASP B 163 -1 N GLY B 160 O GLU B 254 SHEET 1 AA7 2 LYS B 182 PHE B 183 0 SHEET 2 AA7 2 TYR B 192 THR B 193 -1 O TYR B 192 N PHE B 183 SHEET 1 AA8 3 ARG B 305 ARG B 310 0 SHEET 2 AA8 3 GLN B 346 ILE B 351 -1 O ILE B 349 N GLU B 307 SHEET 3 AA8 3 LYS B 337 VAL B 340 -1 N GLU B 339 O GLU B 348 SHEET 1 AA9 4 THR B 410 GLU B 411 0 SHEET 2 AA9 4 LEU B 472 GLU B 476 1 O LYS B 473 N THR B 410 SHEET 3 AA9 4 ALA B 491 TYR B 502 -1 O VAL B 500 N LEU B 474 SHEET 4 AA9 4 ASP B 479 LYS B 483 -1 N ILE B 480 O TYR B 494 SHEET 1 AB1 7 THR B 410 GLU B 411 0 SHEET 2 AB1 7 LEU B 472 GLU B 476 1 O LYS B 473 N THR B 410 SHEET 3 AB1 7 ALA B 491 TYR B 502 -1 O VAL B 500 N LEU B 474 SHEET 4 AB1 7 CYS B 578 ASN B 584 -1 O SER B 579 N TYR B 501 SHEET 5 AB1 7 GLN B 556 LEU B 564 -1 N GLY B 562 O SER B 580 SHEET 6 AB1 7 PHE B 543 ALA B 553 -1 N ILE B 551 O GLY B 559 SHEET 7 AB1 7 VAL B 534 ALA B 537 -1 N LYS B 536 O GLU B 550 SHEET 1 AB2 2 LEU B 417 CYS B 418 0 SHEET 2 AB2 2 VAL B 449 ALA B 450 -1 O VAL B 449 N CYS B 418 CISPEP 1 PHE B 299 PRO B 300 0 16.19 CRYST1 107.904 107.904 279.837 90.00 90.00 90.00 P 43 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 0.009267 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003574 0.00000 CONECT 6812 6818 6819 6820 CONECT 6813 6814 6819 CONECT 6814 6813 6815 6824 6825 CONECT 6815 6814 6816 CONECT 6816 6815 6817 6819 CONECT 6817 6816 6818 6826 CONECT 6818 6812 6817 6832 CONECT 6819 6812 6813 6816 CONECT 6820 6812 6821 CONECT 6821 6820 6822 6823 CONECT 6822 6821 CONECT 6823 6821 CONECT 6824 6814 CONECT 6825 6814 CONECT 6826 6817 6827 6831 CONECT 6827 6826 6828 CONECT 6828 6827 6829 CONECT 6829 6828 6830 CONECT 6830 6829 6831 CONECT 6831 6826 6830 CONECT 6832 6818 6833 6837 CONECT 6833 6832 6834 CONECT 6834 6833 6835 CONECT 6835 6834 6836 6838 CONECT 6836 6835 6837 CONECT 6837 6832 6836 CONECT 6838 6835 MASTER 438 0 1 39 43 0 0 6 6836 2 27 71 END