HEADER LIGASE/ LIGASE INHIBITOR 20-FEB-15 4YCU TITLE CRYSTAL STRUCTURE OF CLADOSPORIN IN COMPLEX WITH HUMAN LYSYL-TRNA TITLE 2 SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE--TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE,LYSRS; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL COMPND 9 PROTEIN 2; COMPND 10 CHAIN: C; COMPND 11 SYNONYM: MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P38,PROTEIN JTV-1; 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: KARS, KIAA0070; 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: AIMP2, JTV1, PRO0992; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, LYSRS, CLADOSPORIN, LIGASE- LIGASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.FANG,J.WANG,M.GUO REVDAT 4 25-DEC-19 4YCU 1 COMPND REVDAT 3 10-OCT-18 4YCU 1 COMPND JRNL REVDAT 2 20-SEP-17 4YCU 1 SOURCE REMARK REVDAT 1 10-JUN-15 4YCU 0 JRNL AUTH P.FANG,H.HAN,J.WANG,K.CHEN,X.CHEN,M.GUO JRNL TITL STRUCTURAL BASIS FOR SPECIFIC INHIBITION OF TRNA SYNTHETASE JRNL TITL 2 BY AN ATP COMPETITIVE INHIBITOR. JRNL REF CHEM. BIOL. V. 22 734 2015 JRNL REFN ISSN 1879-1301 JRNL PMID 26074468 JRNL DOI 10.1016/J.CHEMBIOL.2015.05.007 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 71955 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3602 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 48.1096 - 4.5232 0.99 7461 381 0.1696 0.1831 REMARK 3 2 4.5232 - 3.5906 1.00 7234 404 0.1524 0.1788 REMARK 3 3 3.5906 - 3.1368 1.00 7183 395 0.1859 0.2131 REMARK 3 4 3.1368 - 2.8500 1.00 7244 337 0.2026 0.2114 REMARK 3 5 2.8500 - 2.6458 1.00 7145 393 0.2145 0.2377 REMARK 3 6 2.6458 - 2.4898 1.00 7106 405 0.2219 0.2531 REMARK 3 7 2.4898 - 2.3651 1.00 7203 353 0.2296 0.2729 REMARK 3 8 2.3651 - 2.2621 0.99 7051 366 0.2317 0.2359 REMARK 3 9 2.2621 - 2.1751 0.91 6436 342 0.2379 0.2644 REMARK 3 10 2.1751 - 2.1000 0.60 4290 226 0.2335 0.2647 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.60 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 : 0.006 8556 REMARK 3 ANGLE : 1.045 11580 REMARK 3 CHIRALITY : 0.051 1261 REMARK 3 PLANARITY : 0.005 1498 REMARK 3 DIHEDRAL : 13.222 3239 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): -3.0179 6.9482 30.5169 REMARK 3 T TENSOR REMARK 3 T11: 0.1781 T22: 0.2117 REMARK 3 T33: 0.1712 T12: -0.0576 REMARK 3 T13: -0.0275 T23: 0.0279 REMARK 3 L TENSOR REMARK 3 L11: 0.3215 L22: 0.5497 REMARK 3 L33: 0.5444 L12: -0.0571 REMARK 3 L13: -0.0228 L23: 0.2454 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: -0.0034 S13: 0.0029 REMARK 3 S21: 0.0521 S22: 0.0061 S23: -0.0298 REMARK 3 S31: 0.0994 S32: -0.0193 S33: 0.0047 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 4YCU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75891 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.70900 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000, TRIS, SODIUM CHLORIDE, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 134.49350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 134.49350 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.09700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.92350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.09700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.92350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 134.49350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.09700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.92350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 134.49350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.09700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.92350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 27700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 77880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 990 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1002 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1032 LIES ON A SPECIAL POSITION. 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 69 REMARK 465 SER A 70 REMARK 465 VAL A 71 REMARK 465 ASP A 577 REMARK 465 LYS A 578 REMARK 465 LYS A 579 REMARK 465 GLU A 580 REMARK 465 ASN A 581 REMARK 465 MET B 69 REMARK 465 SER B 70 REMARK 465 VAL B 71 REMARK 465 HIS B 217 REMARK 465 PHE B 218 REMARK 465 GLY B 219 REMARK 465 LEU B 220 REMARK 465 LYS B 221 REMARK 465 GLU B 576 REMARK 465 ASP B 577 REMARK 465 LYS B 578 REMARK 465 LYS B 579 REMARK 465 GLU B 580 REMARK 465 ASN B 581 REMARK 465 MET C 1 REMARK 465 ARG C 33 REMARK 465 SER C 34 REMARK 465 TYR C 35 REMARK 465 GLY C 36 REMARK 465 HIS C 37 REMARK 465 HIS C 38 REMARK 465 HIS C 39 REMARK 465 HIS C 40 REMARK 465 HIS C 41 REMARK 465 HIS C 42 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 LYS A 78 CD CE NZ REMARK 470 ARG A 161 CD NE CZ NH1 NH2 REMARK 470 LYS A 164 NZ REMARK 470 GLU A 166 CD OE1 OE2 REMARK 470 GLU A 167 CD OE1 OE2 REMARK 470 LYS A 192 CD CE NZ REMARK 470 LYS A 193 CD CE NZ REMARK 470 LEU A 216 CG CD1 CD2 REMARK 470 HIS A 217 CG ND1 CD2 CE1 NE2 REMARK 470 PHE A 218 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 LYS A 223 CD CE NZ REMARK 470 ASP A 238 CG OD1 OD2 REMARK 470 GLU A 352 CD OE1 OE2 REMARK 470 LYS A 402 CE NZ REMARK 470 ASN A 412 CG OD1 ND2 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 LYS A 421 CD CE NZ REMARK 470 GLU A 480 CG CD OE1 OE2 REMARK 470 LYS A 517 CD CE NZ REMARK 470 LYS A 519 CD CE NZ REMARK 470 ASP A 524 CG OD1 OD2 REMARK 470 LYS A 574 CG CD CE NZ REMARK 470 GLU A 576 CG CD OE1 OE2 REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 ASP B 123 CG OD1 OD2 REMARK 470 LYS B 153 CD CE NZ REMARK 470 ARG B 161 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 LYS B 192 CG CD CE NZ REMARK 470 LYS B 193 CG CD CE NZ REMARK 470 ASP B 222 CG OD1 OD2 REMARK 470 LYS B 223 CG CD CE NZ REMARK 470 GLU B 224 CG CD OE1 OE2 REMARK 470 GLU B 260 CD OE1 OE2 REMARK 470 GLU B 433 CG CD OE1 OE2 REMARK 470 ASP B 524 CG OD1 OD2 REMARK 470 LYS B 574 CG CD CE NZ REMARK 470 LYS C 7 CD CE NZ 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 CB CYS C 23 SG CYS C 23 4555 1.99 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 GLU A 150 19.87 58.07 REMARK 500 SER A 207 110.22 -165.93 REMARK 500 ALA A 299 147.91 -171.61 REMARK 500 GLU A 325 -155.88 -123.16 REMARK 500 ALA A 520 5.39 -66.65 REMARK 500 TYR B 95 71.19 -118.59 REMARK 500 SER B 207 113.65 -163.89 REMARK 500 ASP B 291 59.39 37.50 REMARK 500 ILE B 457 -65.01 -91.27 REMARK 500 HIS C 10 3.38 -69.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KRS A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KRS B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YCV RELATED DB: PDB REMARK 900 RELATED ID: 4YCW RELATED DB: PDB DBREF 4YCU A 70 581 UNP Q15046 SYK_HUMAN 98 609 DBREF 4YCU B 70 581 UNP Q15046 SYK_HUMAN 98 609 DBREF 4YCU C 1 36 UNP Q13155 AIMP2_HUMAN 1 36 SEQADV 4YCU MET A 69 UNP Q15046 INITIATING METHIONINE SEQADV 4YCU MET B 69 UNP Q15046 INITIATING METHIONINE SEQADV 4YCU HIS C 37 UNP Q13155 EXPRESSION TAG SEQADV 4YCU HIS C 38 UNP Q13155 EXPRESSION TAG SEQADV 4YCU HIS C 39 UNP Q13155 EXPRESSION TAG SEQADV 4YCU HIS C 40 UNP Q13155 EXPRESSION TAG SEQADV 4YCU HIS C 41 UNP Q13155 EXPRESSION TAG SEQADV 4YCU HIS C 42 UNP Q13155 EXPRESSION TAG SEQRES 1 A 513 MET SER VAL ASP PRO ASN GLN TYR TYR LYS ILE ARG SER SEQRES 2 A 513 GLN ALA ILE HIS GLN LEU LYS VAL ASN GLY GLU ASP PRO SEQRES 3 A 513 TYR PRO HIS LYS PHE HIS VAL ASP ILE SER LEU THR ASP SEQRES 4 A 513 PHE ILE GLN LYS TYR SER HIS LEU GLN PRO GLY ASP HIS SEQRES 5 A 513 LEU THR ASP ILE THR LEU LYS VAL ALA GLY ARG ILE HIS SEQRES 6 A 513 ALA LYS ARG ALA SER GLY GLY LYS LEU ILE PHE TYR ASP SEQRES 7 A 513 LEU ARG GLY GLU GLY VAL LYS LEU GLN VAL MET ALA ASN SEQRES 8 A 513 SER ARG ASN TYR LYS SER GLU GLU GLU PHE ILE HIS ILE SEQRES 9 A 513 ASN ASN LYS LEU ARG ARG GLY ASP ILE ILE GLY VAL GLN SEQRES 10 A 513 GLY ASN PRO GLY LYS THR LYS LYS GLY GLU LEU SER ILE SEQRES 11 A 513 ILE PRO TYR GLU ILE THR LEU LEU SER PRO CYS LEU HIS SEQRES 12 A 513 MET LEU PRO HIS LEU HIS PHE GLY LEU LYS ASP LYS GLU SEQRES 13 A 513 THR ARG TYR ARG GLN ARG TYR LEU ASP LEU ILE LEU ASN SEQRES 14 A 513 ASP PHE VAL ARG GLN LYS PHE ILE ILE ARG SER LYS ILE SEQRES 15 A 513 ILE THR TYR ILE ARG SER PHE LEU ASP GLU LEU GLY PHE SEQRES 16 A 513 LEU GLU ILE GLU THR PRO MET MET ASN ILE ILE PRO GLY SEQRES 17 A 513 GLY ALA VAL ALA LYS PRO PHE ILE THR TYR HIS ASN GLU SEQRES 18 A 513 LEU ASP MET ASN LEU TYR MET ARG ILE ALA PRO GLU LEU SEQRES 19 A 513 TYR HIS LYS MET LEU VAL VAL GLY GLY ILE ASP ARG VAL SEQRES 20 A 513 TYR GLU ILE GLY ARG GLN PHE ARG ASN GLU GLY ILE ASP SEQRES 21 A 513 LEU THR HIS ASN PRO GLU PHE THR THR CYS GLU PHE TYR SEQRES 22 A 513 MET ALA TYR ALA ASP TYR HIS ASP LEU MET GLU ILE THR SEQRES 23 A 513 GLU LYS MET VAL SER GLY MET VAL LYS HIS ILE THR GLY SEQRES 24 A 513 SER TYR LYS VAL THR TYR HIS PRO ASP GLY PRO GLU GLY SEQRES 25 A 513 GLN ALA TYR ASP VAL ASP PHE THR PRO PRO PHE ARG ARG SEQRES 26 A 513 ILE ASN MET VAL GLU GLU LEU GLU LYS ALA LEU GLY MET SEQRES 27 A 513 LYS LEU PRO GLU THR ASN LEU PHE GLU THR GLU GLU THR SEQRES 28 A 513 ARG LYS ILE LEU ASP ASP ILE CYS VAL ALA LYS ALA VAL SEQRES 29 A 513 GLU CYS PRO PRO PRO ARG THR THR ALA ARG LEU LEU ASP SEQRES 30 A 513 LYS LEU VAL GLY GLU PHE LEU GLU VAL THR CYS ILE ASN SEQRES 31 A 513 PRO THR PHE ILE CYS ASP HIS PRO GLN ILE MET SER PRO SEQRES 32 A 513 LEU ALA LYS TRP HIS ARG SER LYS GLU GLY LEU THR GLU SEQRES 33 A 513 ARG PHE GLU LEU PHE VAL MET LYS LYS GLU ILE CYS ASN SEQRES 34 A 513 ALA TYR THR GLU LEU ASN ASP PRO MET ARG GLN ARG GLN SEQRES 35 A 513 LEU PHE GLU GLU GLN ALA LYS ALA LYS ALA ALA GLY ASP SEQRES 36 A 513 ASP GLU ALA MET PHE ILE ASP GLU ASN PHE CYS THR ALA SEQRES 37 A 513 LEU GLU TYR GLY LEU PRO PRO THR ALA GLY TRP GLY MET SEQRES 38 A 513 GLY ILE ASP ARG VAL ALA MET PHE LEU THR ASP SER ASN SEQRES 39 A 513 ASN ILE LYS GLU VAL LEU LEU PHE PRO ALA MET LYS PRO SEQRES 40 A 513 GLU ASP LYS LYS GLU ASN SEQRES 1 B 513 MET SER VAL ASP PRO ASN GLN TYR TYR LYS ILE ARG SER SEQRES 2 B 513 GLN ALA ILE HIS GLN LEU LYS VAL ASN GLY GLU ASP PRO SEQRES 3 B 513 TYR PRO HIS LYS PHE HIS VAL ASP ILE SER LEU THR ASP SEQRES 4 B 513 PHE ILE GLN LYS TYR SER HIS LEU GLN PRO GLY ASP HIS SEQRES 5 B 513 LEU THR ASP ILE THR LEU LYS VAL ALA GLY ARG ILE HIS SEQRES 6 B 513 ALA LYS ARG ALA SER GLY GLY LYS LEU ILE PHE TYR ASP SEQRES 7 B 513 LEU ARG GLY GLU GLY VAL LYS LEU GLN VAL MET ALA ASN SEQRES 8 B 513 SER ARG ASN TYR LYS SER GLU GLU GLU PHE ILE HIS ILE SEQRES 9 B 513 ASN ASN LYS LEU ARG ARG GLY ASP ILE ILE GLY VAL GLN SEQRES 10 B 513 GLY ASN PRO GLY LYS THR LYS LYS GLY GLU LEU SER ILE SEQRES 11 B 513 ILE PRO TYR GLU ILE THR LEU LEU SER PRO CYS LEU HIS SEQRES 12 B 513 MET LEU PRO HIS LEU HIS PHE GLY LEU LYS ASP LYS GLU SEQRES 13 B 513 THR ARG TYR ARG GLN ARG TYR LEU ASP LEU ILE LEU ASN SEQRES 14 B 513 ASP PHE VAL ARG GLN LYS PHE ILE ILE ARG SER LYS ILE SEQRES 15 B 513 ILE THR TYR ILE ARG SER PHE LEU ASP GLU LEU GLY PHE SEQRES 16 B 513 LEU GLU ILE GLU THR PRO MET MET ASN ILE ILE PRO GLY SEQRES 17 B 513 GLY ALA VAL ALA LYS PRO PHE ILE THR TYR HIS ASN GLU SEQRES 18 B 513 LEU ASP MET ASN LEU TYR MET ARG ILE ALA PRO GLU LEU SEQRES 19 B 513 TYR HIS LYS MET LEU VAL VAL GLY GLY ILE ASP ARG VAL SEQRES 20 B 513 TYR GLU ILE GLY ARG GLN PHE ARG ASN GLU GLY ILE ASP SEQRES 21 B 513 LEU THR HIS ASN PRO GLU PHE THR THR CYS GLU PHE TYR SEQRES 22 B 513 MET ALA TYR ALA ASP TYR HIS ASP LEU MET GLU ILE THR SEQRES 23 B 513 GLU LYS MET VAL SER GLY MET VAL LYS HIS ILE THR GLY SEQRES 24 B 513 SER TYR LYS VAL THR TYR HIS PRO ASP GLY PRO GLU GLY SEQRES 25 B 513 GLN ALA TYR ASP VAL ASP PHE THR PRO PRO PHE ARG ARG SEQRES 26 B 513 ILE ASN MET VAL GLU GLU LEU GLU LYS ALA LEU GLY MET SEQRES 27 B 513 LYS LEU PRO GLU THR ASN LEU PHE GLU THR GLU GLU THR SEQRES 28 B 513 ARG LYS ILE LEU ASP ASP ILE CYS VAL ALA LYS ALA VAL SEQRES 29 B 513 GLU CYS PRO PRO PRO ARG THR THR ALA ARG LEU LEU ASP SEQRES 30 B 513 LYS LEU VAL GLY GLU PHE LEU GLU VAL THR CYS ILE ASN SEQRES 31 B 513 PRO THR PHE ILE CYS ASP HIS PRO GLN ILE MET SER PRO SEQRES 32 B 513 LEU ALA LYS TRP HIS ARG SER LYS GLU GLY LEU THR GLU SEQRES 33 B 513 ARG PHE GLU LEU PHE VAL MET LYS LYS GLU ILE CYS ASN SEQRES 34 B 513 ALA TYR THR GLU LEU ASN ASP PRO MET ARG GLN ARG GLN SEQRES 35 B 513 LEU PHE GLU GLU GLN ALA LYS ALA LYS ALA ALA GLY ASP SEQRES 36 B 513 ASP GLU ALA MET PHE ILE ASP GLU ASN PHE CYS THR ALA SEQRES 37 B 513 LEU GLU TYR GLY LEU PRO PRO THR ALA GLY TRP GLY MET SEQRES 38 B 513 GLY ILE ASP ARG VAL ALA MET PHE LEU THR ASP SER ASN SEQRES 39 B 513 ASN ILE LYS GLU VAL LEU LEU PHE PRO ALA MET LYS PRO SEQRES 40 B 513 GLU ASP LYS LYS GLU ASN SEQRES 1 C 42 MET PRO MET TYR GLN VAL LYS PRO TYR HIS GLY GLY GLY SEQRES 2 C 42 ALA PRO LEU ARG VAL GLU LEU PRO THR CYS MET TYR ARG SEQRES 3 C 42 LEU PRO ASN VAL HIS GLY ARG SER TYR GLY HIS HIS HIS SEQRES 4 C 42 HIS HIS HIS HET KRS A 601 21 HET LYS A 602 10 HET GOL A 603 6 HET GOL A 604 6 HET KRS B 601 21 HET LYS B 602 10 HET GOL B 603 6 HET GOL B 604 6 HETNAM KRS CLADOSPORIN HETNAM LYS LYSINE HETNAM GOL GLYCEROL HETSYN KRS (3R)-3-[[(2R,6S)-6-METHYLOXAN-2-YL]METHYL]-6,8- HETSYN 2 KRS BIS(OXIDANYL)-3,4-DIHYDROISOCHROMEN-1-ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 KRS 2(C16 H20 O5) FORMUL 5 LYS 2(C6 H15 N2 O2 1+) FORMUL 6 GOL 4(C3 H8 O3) FORMUL 12 HOH *696(H2 O) HELIX 1 AA1 ASP A 72 ASN A 90 1 19 HELIX 2 AA2 SER A 104 SER A 113 1 10 HELIX 3 AA3 ARG A 161 TYR A 163 5 3 HELIX 4 AA4 SER A 165 LEU A 176 1 12 HELIX 5 AA5 ASP A 222 GLN A 229 1 8 HELIX 6 AA6 GLN A 229 ASN A 237 1 9 HELIX 7 AA7 ASN A 237 LEU A 261 1 25 HELIX 8 AA8 PRO A 300 GLY A 310 1 11 HELIX 9 AA9 ASP A 346 GLY A 367 1 22 HELIX 10 AB1 MET A 396 GLY A 405 1 10 HELIX 11 AB2 THR A 416 LYS A 430 1 15 HELIX 12 AB3 THR A 439 LEU A 452 1 14 HELIX 13 AB4 GLU A 453 CYS A 456 5 4 HELIX 14 AB5 PRO A 466 SER A 470 5 5 HELIX 15 AB6 ASP A 504 ALA A 520 1 17 HELIX 16 AB7 ASP A 530 TYR A 539 1 10 HELIX 17 AB8 ILE A 551 THR A 559 1 9 HELIX 18 AB9 ASN A 563 LEU A 568 5 6 HELIX 19 AC1 PRO B 73 ASN B 90 1 18 HELIX 20 AC2 SER B 104 SER B 113 1 10 HELIX 21 AC3 SER B 165 LEU B 176 1 12 HELIX 22 AC4 LYS B 223 GLN B 229 1 7 HELIX 23 AC5 GLN B 229 ASN B 237 1 9 HELIX 24 AC6 ASN B 237 LEU B 261 1 25 HELIX 25 AC7 PRO B 300 GLY B 310 1 11 HELIX 26 AC8 ASP B 346 GLY B 367 1 22 HELIX 27 AC9 MET B 396 GLY B 405 1 10 HELIX 28 AD1 GLU B 410 PHE B 414 5 5 HELIX 29 AD2 THR B 416 LYS B 430 1 15 HELIX 30 AD3 THR B 439 LEU B 452 1 14 HELIX 31 AD4 GLU B 453 CYS B 456 5 4 HELIX 32 AD5 PRO B 466 SER B 470 5 5 HELIX 33 AD6 ASP B 504 GLY B 522 1 19 HELIX 34 AD7 ASP B 530 GLU B 538 1 9 HELIX 35 AD8 ILE B 551 THR B 559 1 9 HELIX 36 AD9 ASN B 563 LEU B 568 5 6 SHEET 1 AA1 6 LEU A 126 ALA A 137 0 SHEET 2 AA1 6 LEU A 142 GLY A 149 -1 O PHE A 144 N ARG A 136 SHEET 3 AA1 6 VAL A 152 ASN A 159 -1 O VAL A 156 N TYR A 145 SHEET 4 AA1 6 LEU A 196 SER A 207 1 O ILE A 198 N GLN A 155 SHEET 5 AA1 6 ILE A 181 LYS A 190 -1 N GLN A 185 O TYR A 201 SHEET 6 AA1 6 LEU A 126 ALA A 137 -1 N VAL A 128 O VAL A 184 SHEET 1 AA2 8 LEU A 264 GLU A 265 0 SHEET 2 AA2 8 ARG A 314 PHE A 322 1 O ARG A 314 N LEU A 264 SHEET 3 AA2 8 GLU A 334 ALA A 343 -1 O PHE A 335 N GLN A 321 SHEET 4 AA2 8 THR A 544 GLY A 550 -1 O ALA A 545 N MET A 342 SHEET 5 AA2 8 LYS A 493 THR A 500 -1 N TYR A 499 O GLY A 546 SHEET 6 AA2 8 ARG A 485 VAL A 490 -1 N PHE A 486 O ALA A 498 SHEET 7 AA2 8 THR A 460 CYS A 463 -1 N THR A 460 O PHE A 489 SHEET 8 AA2 8 ARG A 392 ASN A 395 1 N ARG A 392 O PHE A 461 SHEET 1 AA3 3 MET A 271 ASN A 272 0 SHEET 2 AA3 3 MET A 292 MET A 296 -1 O TYR A 295 N ASN A 272 SHEET 3 AA3 3 ILE A 284 HIS A 287 -1 N THR A 285 O LEU A 294 SHEET 1 AA4 2 LYS A 370 TYR A 373 0 SHEET 2 AA4 2 TYR A 383 ASP A 386 -1 O VAL A 385 N VAL A 371 SHEET 1 AA5 6 LEU B 126 ALA B 137 0 SHEET 2 AA5 6 LEU B 142 GLY B 149 -1 O PHE B 144 N ARG B 136 SHEET 3 AA5 6 VAL B 152 ASN B 159 -1 O LEU B 154 N LEU B 147 SHEET 4 AA5 6 LEU B 196 SER B 207 1 O ILE B 198 N GLN B 155 SHEET 5 AA5 6 ILE B 181 LYS B 190 -1 N GLN B 185 O TYR B 201 SHEET 6 AA5 6 LEU B 126 ALA B 137 -1 N VAL B 128 O VAL B 184 SHEET 1 AA6 8 LEU B 264 GLU B 265 0 SHEET 2 AA6 8 ARG B 314 PHE B 322 1 O ARG B 314 N LEU B 264 SHEET 3 AA6 8 GLU B 334 ALA B 343 -1 O PHE B 335 N GLN B 321 SHEET 4 AA6 8 THR B 544 GLY B 550 -1 O ALA B 545 N MET B 342 SHEET 5 AA6 8 LYS B 493 THR B 500 -1 N ILE B 495 O GLY B 550 SHEET 6 AA6 8 ARG B 485 VAL B 490 -1 N LEU B 488 O ILE B 495 SHEET 7 AA6 8 THR B 460 CYS B 463 -1 N ILE B 462 O GLU B 487 SHEET 8 AA6 8 ARG B 392 ASN B 395 1 N ARG B 392 O PHE B 461 SHEET 1 AA7 3 MET B 271 ASN B 272 0 SHEET 2 AA7 3 MET B 292 MET B 296 -1 O TYR B 295 N ASN B 272 SHEET 3 AA7 3 ILE B 284 HIS B 287 -1 N THR B 285 O LEU B 294 SHEET 1 AA8 2 LYS B 370 TYR B 373 0 SHEET 2 AA8 2 TYR B 383 ASP B 386 -1 O VAL B 385 N VAL B 371 SSBOND 1 CYS C 23 CYS C 23 1555 4555 2.08 CISPEP 1 GLY A 219 LEU A 220 0 -12.80 CISPEP 2 PRO A 389 PRO A 390 0 0.80 CISPEP 3 PRO A 436 PRO A 437 0 -4.57 CISPEP 4 PRO B 389 PRO B 390 0 2.20 CISPEP 5 PRO B 436 PRO B 437 0 1.75 SITE 1 AC1 13 ARG A 323 GLU A 325 HIS A 331 ASN A 332 SITE 2 AC1 13 PHE A 335 THR A 337 GLU A 494 ILE A 495 SITE 3 AC1 13 GLY A 550 ARG A 553 LYS A 602 HOH A 757 SITE 4 AC1 13 HOH A 863 SITE 1 AC2 12 GLY A 277 GLU A 301 ARG A 323 GLU A 339 SITE 2 AC2 12 TYR A 341 ASN A 497 TYR A 499 GLU A 501 SITE 3 AC2 12 GLY A 546 GLY A 548 KRS A 601 HOH A 748 SITE 1 AC3 10 ARG A 131 HIS A 133 GLY A 149 GLU A 150 SITE 2 AC3 10 GLY A 151 ILE A 235 ARG A 241 HOH A 803 SITE 3 AC3 10 HOH A 872 HOH A 919 SITE 1 AC4 3 ASP A 445 GLU A 453 GLU A 487 SITE 1 AC5 14 ARG B 323 GLU B 325 HIS B 331 ASN B 332 SITE 2 AC5 14 PHE B 335 THR B 337 GLU B 494 ILE B 495 SITE 3 AC5 14 CYS B 496 GLY B 550 ARG B 553 LYS B 602 SITE 4 AC5 14 HOH B 826 HOH B 896 SITE 1 AC6 11 GLY B 277 GLU B 301 ARG B 323 GLU B 339 SITE 2 AC6 11 TYR B 341 ASN B 497 TYR B 499 GLU B 501 SITE 3 AC6 11 GLY B 546 KRS B 601 HOH B 760 SITE 1 AC7 7 TYR B 347 MET B 351 ARG B 393 ASN B 395 SITE 2 AC7 7 CYS B 463 ASP B 464 HOH B 852 SITE 1 AC8 5 ASP B 445 GLU B 453 GLU B 487 GLU B 494 SITE 2 AC8 5 HOH B 739 CRYST1 96.194 99.847 268.987 90.00 90.00 90.00 C 2 2 21 16 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 0.010396 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003718 0.00000