HEADER LIGASE 01-AUG-23 8K9W TITLE CRYSTAL STRUCTURE OF PLASMODIUM LYSRS COMPLEXING WITH ASP3026 DERIVED TITLE 2 LYSRS INHIBITOR 4 (ADKI4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE--TRNA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE CAMP / SOURCE 3 MALAYSIA); SOURCE 4 ORGANISM_TAXID: 5835; SOURCE 5 GENE: PFMC_04735; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYSYL-TRNA SYNTHETASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHOU,M.XIA,G.YANG,P.LI,P.FANG REVDAT 3 23-OCT-24 8K9W 1 REMARK REVDAT 2 03-JUL-24 8K9W 1 JRNL REVDAT 1 26-JUN-24 8K9W 0 JRNL AUTH J.ZHOU,M.XIA,Z.HUANG,H.QIAO,G.YANG,Y.QIAN,P.LI,Z.ZHANG, JRNL AUTH 2 X.GAO,L.JIANG,J.WANG,W.LI,P.FANG JRNL TITL STRUCTURE-GUIDED CONVERSION FROM AN ANAPLASTIC LYMPHOMA JRNL TITL 2 KINASE INHIBITOR INTO PLASMODIUM LYSYL-TRNA SYNTHETASE JRNL TITL 3 SELECTIVE INHIBITORS. JRNL REF COMMUN BIOL V. 7 742 2024 JRNL REFN ESSN 2399-3642 JRNL PMID 38890421 JRNL DOI 10.1038/S42003-024-06455-4 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 52243 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 32.4500 - 4.9500 1.00 5282 211 0.1963 0.2279 REMARK 3 2 4.9500 - 3.9300 1.00 5086 202 0.1729 0.2059 REMARK 3 3 3.9300 - 3.4300 1.00 5022 200 0.2109 0.2471 REMARK 3 4 3.4300 - 3.1200 1.00 5027 200 0.2369 0.2715 REMARK 3 5 3.1200 - 2.9000 1.00 4989 198 0.2510 0.2791 REMARK 3 6 2.9000 - 2.7300 1.00 4990 200 0.2641 0.3288 REMARK 3 7 2.7300 - 2.5900 1.00 4970 197 0.2810 0.3314 REMARK 3 8 2.5900 - 2.4800 1.00 4969 198 0.2693 0.3306 REMARK 3 9 2.4800 - 2.3800 1.00 4960 197 0.2839 0.3301 REMARK 3 10 2.3800 - 2.3000 1.00 4948 197 0.2902 0.3232 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.260 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 : 0.006 7784 REMARK 3 ANGLE : 0.847 10577 REMARK 3 CHIRALITY : 0.053 1161 REMARK 3 PLANARITY : 0.007 1368 REMARK 3 DIHEDRAL : 15.801 2809 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): -9.7955 -6.0474 35.3794 REMARK 3 T TENSOR REMARK 3 T11: 0.4308 T22: 0.3649 REMARK 3 T33: 0.5117 T12: -0.1041 REMARK 3 T13: -0.0768 T23: 0.0318 REMARK 3 L TENSOR REMARK 3 L11: 0.5306 L22: 0.9028 REMARK 3 L33: 2.6018 L12: -0.1077 REMARK 3 L13: -0.1052 L23: -0.6237 REMARK 3 S TENSOR REMARK 3 S11: -0.0630 S12: -0.0080 S13: 0.0338 REMARK 3 S21: -0.0109 S22: -0.1386 S23: -0.1859 REMARK 3 S31: -0.1976 S32: 0.1964 S33: 0.1785 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 8K9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 09-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.979098 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52342 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 1.12800 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES PH 6.0, PEG4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 35.95800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.12650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.77550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 84.12650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.95800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.77550 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 76 REMARK 465 GLU A 77 REMARK 465 ALA A 144 REMARK 465 SER A 145 REMARK 465 GLY A 146 REMARK 465 TYR A 225 REMARK 465 GLY A 226 REMARK 465 LEU A 227 REMARK 465 LYS A 228 REMARK 465 ASP A 229 REMARK 465 GLY A 283 REMARK 465 GLY A 284 REMARK 465 ALA A 285 REMARK 465 LYS A 519 REMARK 465 LEU A 520 REMARK 465 GLN A 521 REMARK 465 GLN A 522 REMARK 465 LYS A 523 REMARK 465 ASP A 524 REMARK 465 ARG A 525 REMARK 465 GLU A 526 REMARK 465 LYS A 527 REMARK 465 GLY A 528 REMARK 465 ASP A 529 REMARK 465 THR A 530 REMARK 465 GLU A 531 REMARK 465 ALA A 532 REMARK 465 ALA A 533 REMARK 465 GLN A 534 REMARK 465 LEU A 535 REMARK 465 ALA A 582 REMARK 465 ASN A 583 REMARK 465 GLY A 584 REMARK 465 GLY A 585 REMARK 465 HIS A 586 REMARK 465 HIS A 587 REMARK 465 HIS A 588 REMARK 465 HIS A 589 REMARK 465 HIS A 590 REMARK 465 HIS A 591 REMARK 465 MET B 76 REMARK 465 GLU B 77 REMARK 465 SER B 145 REMARK 465 GLY B 146 REMARK 465 GLY B 283 REMARK 465 GLY B 284 REMARK 465 ALA B 285 REMARK 465 LYS B 519 REMARK 465 LEU B 520 REMARK 465 GLN B 521 REMARK 465 GLN B 522 REMARK 465 LYS B 523 REMARK 465 ASP B 524 REMARK 465 ARG B 525 REMARK 465 GLU B 526 REMARK 465 LYS B 527 REMARK 465 GLY B 528 REMARK 465 ASP B 529 REMARK 465 THR B 530 REMARK 465 GLU B 531 REMARK 465 ALA B 532 REMARK 465 ALA B 533 REMARK 465 GLN B 534 REMARK 465 LEU B 535 REMARK 465 ALA B 582 REMARK 465 ASN B 583 REMARK 465 GLY B 584 REMARK 465 GLY B 585 REMARK 465 HIS B 586 REMARK 465 HIS B 587 REMARK 465 HIS B 588 REMARK 465 HIS B 589 REMARK 465 HIS B 590 REMARK 465 HIS B 591 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 VAL A 78 CG1 CG2 REMARK 470 ASP A 79 CG OD1 OD2 REMARK 470 ARG A 81 CD NE CZ NH1 NH2 REMARK 470 LYS A 89 CD CE NZ REMARK 470 LYS A 97 CD CE NZ REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 GLN A 147 CG CD OE1 NE2 REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 LYS A 198 CG CD CE NZ REMARK 470 LYS A 200 CG CD CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 MET A 220 CG SD CE REMARK 470 MET A 223 CG SD CE REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 THR A 230 OG1 CG2 REMARK 470 GLU A 231 CG CD OE1 OE2 REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 ILE A 281 CG1 CG2 CD1 REMARK 470 ASN A 286 CG OD1 ND2 REMARK 470 LEU A 299 CG CD1 CD2 REMARK 470 LYS A 382 CG CD CE NZ REMARK 470 ASP A 383 CG OD1 OD2 REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 GLN A 388 CG CD OE1 NE2 REMARK 470 LYS A 409 CG CD CE NZ REMARK 470 GLU A 416 CG CD OE1 OE2 REMARK 470 GLN A 417 CG CD OE1 NE2 REMARK 470 GLU A 423 CG CD OE1 OE2 REMARK 470 GLU A 426 CG CD OE1 OE2 REMARK 470 LYS A 427 CG CD CE NZ REMARK 470 LYS A 433 CG CD CE NZ REMARK 470 GLU A 434 CG CD OE1 OE2 REMARK 470 LYS A 436 CG CD CE NZ REMARK 470 LYS A 447 CD CE NZ REMARK 470 LYS A 460 CG CD CE NZ REMARK 470 ARG A 483 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 515 CG CD CE NZ REMARK 470 GLU A 516 CG CD OE1 OE2 REMARK 470 PHE A 518 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 536 CG OD1 OD2 REMARK 470 LYS A 571 CG CD CE NZ REMARK 470 ARG A 580 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 78 CG1 CG2 REMARK 470 ASP B 79 CG OD1 OD2 REMARK 470 ARG B 81 CD NE CZ NH1 NH2 REMARK 470 LEU B 82 CG CD1 CD2 REMARK 470 GLU B 85 CG CD OE1 OE2 REMARK 470 LYS B 89 CD CE NZ REMARK 470 LYS B 97 CD CE NZ REMARK 470 LYS B 105 CG CD CE NZ REMARK 470 LYS B 118 CD CE NZ REMARK 470 ASP B 121 CG OD1 OD2 REMARK 470 GLN B 147 CG CD OE1 NE2 REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 GLN B 162 CG CD OE1 NE2 REMARK 470 LYS B 183 CG CD CE NZ REMARK 470 LYS B 200 CG CD CE NZ REMARK 470 LYS B 201 CG CD CE NZ REMARK 470 GLU B 203 CG CD OE1 OE2 REMARK 470 LYS B 228 CG CD CE NZ REMARK 470 ASP B 229 CG OD1 OD2 REMARK 470 THR B 230 OG1 CG2 REMARK 470 ILE B 281 CG1 CG2 CD1 REMARK 470 ASN B 286 CG OD1 ND2 REMARK 470 ASP B 296 CG OD1 OD2 REMARK 470 LEU B 297 CG CD1 CD2 REMARK 470 ASP B 298 CG OD1 OD2 REMARK 470 LEU B 299 CG CD1 CD2 REMARK 470 LYS B 382 CE NZ REMARK 470 LYS B 409 CG CD CE NZ REMARK 470 GLU B 416 CG CD OE1 OE2 REMARK 470 GLN B 417 CG CD OE1 NE2 REMARK 470 GLU B 423 CG CD OE1 OE2 REMARK 470 GLU B 426 CG CD OE1 OE2 REMARK 470 LYS B 427 CG CD CE NZ REMARK 470 ASN B 430 CG OD1 ND2 REMARK 470 LYS B 433 CG CD CE NZ REMARK 470 GLU B 434 CG CD OE1 OE2 REMARK 470 LYS B 436 CG CD CE NZ REMARK 470 ILE B 437 CG1 CG2 CD1 REMARK 470 GLU B 438 CG CD OE1 OE2 REMARK 470 LEU B 439 CG CD1 CD2 REMARK 470 ASN B 441 CG OD1 ND2 REMARK 470 LYS B 447 CG CD CE NZ REMARK 470 LEU B 448 CG CD1 CD2 REMARK 470 GLN B 451 CG CD OE1 NE2 REMARK 470 HIS B 455 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 460 CG CD CE NZ REMARK 470 LYS B 513 CG CD CE NZ REMARK 470 LYS B 515 CG CD CE NZ REMARK 470 GLU B 516 CG CD OE1 OE2 REMARK 470 PHE B 518 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP B 536 CG OD1 OD2 REMARK 470 LYS B 571 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 ASP A 96 2.40 -67.52 REMARK 500 GLN A 417 -68.89 -29.82 REMARK 500 PRO A 418 98.58 -64.73 REMARK 500 ILE A 457 -52.26 -124.42 REMARK 500 TYR B 119 16.84 -140.37 REMARK 500 LEU B 128 75.49 -105.01 REMARK 500 GLU B 129 0.70 -69.04 REMARK 500 LEU B 227 65.85 -101.86 REMARK 500 GLU B 332 -168.31 -128.22 REMARK 500 LYS B 436 64.96 64.35 REMARK 500 GLU B 490 49.92 -95.29 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 235 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF1 8K9W A 77 583 UNP A0A024X378_PLAFC DBREF2 8K9W A A0A024X378 77 583 DBREF1 8K9W B 77 583 UNP A0A024X378_PLAFC DBREF2 8K9W B A0A024X378 77 583 SEQADV 8K9W MET A 76 UNP A0A024X37 INITIATING METHIONINE SEQADV 8K9W GLY A 584 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W GLY A 585 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS A 586 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS A 587 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS A 588 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS A 589 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS A 590 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS A 591 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W MET B 76 UNP A0A024X37 INITIATING METHIONINE SEQADV 8K9W GLY B 584 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W GLY B 585 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS B 586 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS B 587 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS B 588 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS B 589 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS B 590 UNP A0A024X37 EXPRESSION TAG SEQADV 8K9W HIS B 591 UNP A0A024X37 EXPRESSION TAG SEQRES 1 A 516 MET GLU VAL ASP PRO ARG LEU TYR PHE GLU ASN ARG SER SEQRES 2 A 516 LYS PHE ILE GLN ASP GLN LYS ASP LYS GLY ILE ASN PRO SEQRES 3 A 516 TYR PRO HIS LYS PHE GLU ARG THR ILE SER ILE PRO GLU SEQRES 4 A 516 PHE ILE GLU LYS TYR LYS ASP LEU GLY ASN GLY GLU HIS SEQRES 5 A 516 LEU GLU ASP THR ILE LEU ASN ILE THR GLY ARG ILE MET SEQRES 6 A 516 ARG VAL SER ALA SER GLY GLN LYS LEU ARG PHE PHE ASP SEQRES 7 A 516 LEU VAL GLY ASP GLY GLU LYS ILE GLN VAL LEU ALA ASN SEQRES 8 A 516 TYR SER PHE HIS ASN HIS GLU LYS GLY ASN PHE ALA GLU SEQRES 9 A 516 CYS TYR ASP LYS ILE ARG ARG GLY ASP ILE VAL GLY ILE SEQRES 10 A 516 VAL GLY PHE PRO GLY LYS SER LYS LYS GLY GLU LEU SER SEQRES 11 A 516 ILE PHE PRO LYS GLU THR ILE LEU LEU SER ALA CYS LEU SEQRES 12 A 516 HIS MET LEU PRO MET LYS TYR GLY LEU LYS ASP THR GLU SEQRES 13 A 516 ILE ARG TYR ARG GLN ARG TYR LEU ASP LEU LEU ILE ASN SEQRES 14 A 516 GLU SER SER ARG HIS THR PHE VAL THR ARG THR LYS ILE SEQRES 15 A 516 ILE ASN PHE LEU ARG ASN PHE LEU ASN GLU ARG GLY PHE SEQRES 16 A 516 PHE GLU VAL GLU THR PRO MET MET ASN LEU ILE ALA GLY SEQRES 17 A 516 GLY ALA ASN ALA ARG PRO PHE ILE THR HIS HIS ASN ASP SEQRES 18 A 516 LEU ASP LEU ASP LEU TYR LEU ARG ILE ALA THR GLU LEU SEQRES 19 A 516 PRO LEU LYS MET LEU ILE VAL GLY GLY ILE ASP LYS VAL SEQRES 20 A 516 TYR GLU ILE GLY LYS VAL PHE ARG ASN GLU GLY ILE ASP SEQRES 21 A 516 ASN THR HIS ASN PRO GLU PHE THR SER CYS GLU PHE TYR SEQRES 22 A 516 TRP ALA TYR ALA ASP TYR ASN ASP LEU ILE LYS TRP SER SEQRES 23 A 516 GLU ASP PHE PHE SER GLN LEU VAL TYR HIS LEU PHE GLY SEQRES 24 A 516 THR TYR LYS ILE SER TYR ASN LYS ASP GLY PRO GLU ASN SEQRES 25 A 516 GLN PRO ILE GLU ILE ASP PHE THR PRO PRO TYR PRO LYS SEQRES 26 A 516 VAL SER ILE VAL GLU GLU ILE GLU LYS VAL THR ASN THR SEQRES 27 A 516 ILE LEU GLU GLN PRO PHE ASP SER ASN GLU THR ILE GLU SEQRES 28 A 516 LYS MET ILE ASN ILE ILE LYS GLU HIS LYS ILE GLU LEU SEQRES 29 A 516 PRO ASN PRO PRO THR ALA ALA LYS LEU LEU ASP GLN LEU SEQRES 30 A 516 ALA SER HIS PHE ILE GLU ASN LYS TYR ASN ASP LYS PRO SEQRES 31 A 516 PHE PHE ILE VAL GLU HIS PRO GLN ILE MET SER PRO LEU SEQRES 32 A 516 ALA LYS TYR HIS ARG THR LYS PRO GLY LEU THR GLU ARG SEQRES 33 A 516 LEU GLU MET PHE ILE CYS GLY LYS GLU VAL LEU ASN ALA SEQRES 34 A 516 TYR THR GLU LEU ASN ASP PRO PHE LYS GLN LYS GLU CYS SEQRES 35 A 516 PHE LYS LEU GLN GLN LYS ASP ARG GLU LYS GLY ASP THR SEQRES 36 A 516 GLU ALA ALA GLN LEU ASP SER ALA PHE CYS THR SER LEU SEQRES 37 A 516 GLU TYR GLY LEU PRO PRO THR GLY GLY LEU GLY LEU GLY SEQRES 38 A 516 ILE ASP ARG ILE THR MET PHE LEU THR ASN LYS ASN SER SEQRES 39 A 516 ILE LYS ASP VAL ILE LEU PHE PRO THR MET ARG PRO ALA SEQRES 40 A 516 ASN GLY GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 516 MET GLU VAL ASP PRO ARG LEU TYR PHE GLU ASN ARG SER SEQRES 2 B 516 LYS PHE ILE GLN ASP GLN LYS ASP LYS GLY ILE ASN PRO SEQRES 3 B 516 TYR PRO HIS LYS PHE GLU ARG THR ILE SER ILE PRO GLU SEQRES 4 B 516 PHE ILE GLU LYS TYR LYS ASP LEU GLY ASN GLY GLU HIS SEQRES 5 B 516 LEU GLU ASP THR ILE LEU ASN ILE THR GLY ARG ILE MET SEQRES 6 B 516 ARG VAL SER ALA SER GLY GLN LYS LEU ARG PHE PHE ASP SEQRES 7 B 516 LEU VAL GLY ASP GLY GLU LYS ILE GLN VAL LEU ALA ASN SEQRES 8 B 516 TYR SER PHE HIS ASN HIS GLU LYS GLY ASN PHE ALA GLU SEQRES 9 B 516 CYS TYR ASP LYS ILE ARG ARG GLY ASP ILE VAL GLY ILE SEQRES 10 B 516 VAL GLY PHE PRO GLY LYS SER LYS LYS GLY GLU LEU SER SEQRES 11 B 516 ILE PHE PRO LYS GLU THR ILE LEU LEU SER ALA CYS LEU SEQRES 12 B 516 HIS MET LEU PRO MET LYS TYR GLY LEU LYS ASP THR GLU SEQRES 13 B 516 ILE ARG TYR ARG GLN ARG TYR LEU ASP LEU LEU ILE ASN SEQRES 14 B 516 GLU SER SER ARG HIS THR PHE VAL THR ARG THR LYS ILE SEQRES 15 B 516 ILE ASN PHE LEU ARG ASN PHE LEU ASN GLU ARG GLY PHE SEQRES 16 B 516 PHE GLU VAL GLU THR PRO MET MET ASN LEU ILE ALA GLY SEQRES 17 B 516 GLY ALA ASN ALA ARG PRO PHE ILE THR HIS HIS ASN ASP SEQRES 18 B 516 LEU ASP LEU ASP LEU TYR LEU ARG ILE ALA THR GLU LEU SEQRES 19 B 516 PRO LEU LYS MET LEU ILE VAL GLY GLY ILE ASP LYS VAL SEQRES 20 B 516 TYR GLU ILE GLY LYS VAL PHE ARG ASN GLU GLY ILE ASP SEQRES 21 B 516 ASN THR HIS ASN PRO GLU PHE THR SER CYS GLU PHE TYR SEQRES 22 B 516 TRP ALA TYR ALA ASP TYR ASN ASP LEU ILE LYS TRP SER SEQRES 23 B 516 GLU ASP PHE PHE SER GLN LEU VAL TYR HIS LEU PHE GLY SEQRES 24 B 516 THR TYR LYS ILE SER TYR ASN LYS ASP GLY PRO GLU ASN SEQRES 25 B 516 GLN PRO ILE GLU ILE ASP PHE THR PRO PRO TYR PRO LYS SEQRES 26 B 516 VAL SER ILE VAL GLU GLU ILE GLU LYS VAL THR ASN THR SEQRES 27 B 516 ILE LEU GLU GLN PRO PHE ASP SER ASN GLU THR ILE GLU SEQRES 28 B 516 LYS MET ILE ASN ILE ILE LYS GLU HIS LYS ILE GLU LEU SEQRES 29 B 516 PRO ASN PRO PRO THR ALA ALA LYS LEU LEU ASP GLN LEU SEQRES 30 B 516 ALA SER HIS PHE ILE GLU ASN LYS TYR ASN ASP LYS PRO SEQRES 31 B 516 PHE PHE ILE VAL GLU HIS PRO GLN ILE MET SER PRO LEU SEQRES 32 B 516 ALA LYS TYR HIS ARG THR LYS PRO GLY LEU THR GLU ARG SEQRES 33 B 516 LEU GLU MET PHE ILE CYS GLY LYS GLU VAL LEU ASN ALA SEQRES 34 B 516 TYR THR GLU LEU ASN ASP PRO PHE LYS GLN LYS GLU CYS SEQRES 35 B 516 PHE LYS LEU GLN GLN LYS ASP ARG GLU LYS GLY ASP THR SEQRES 36 B 516 GLU ALA ALA GLN LEU ASP SER ALA PHE CYS THR SER LEU SEQRES 37 B 516 GLU TYR GLY LEU PRO PRO THR GLY GLY LEU GLY LEU GLY SEQRES 38 B 516 ILE ASP ARG ILE THR MET PHE LEU THR ASN LYS ASN SER SEQRES 39 B 516 ILE LYS ASP VAL ILE LEU PHE PRO THR MET ARG PRO ALA SEQRES 40 B 516 ASN GLY GLY HIS HIS HIS HIS HIS HIS HET JTR A 601 28 HET MES A 602 12 HET MES A 603 12 HET JTR B 601 28 HETNAM JTR ~{N}2-(2-METHOXYPHENYL)-~{N}4-(2-PROPAN-2- HETNAM 2 JTR YLSULFONYLPHENYL)-1,3,5-TRIAZINE-2,4-DIAMINE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 3 JTR 2(C19 H21 N5 O3 S) FORMUL 4 MES 2(C6 H13 N O4 S) FORMUL 7 HOH *136(H2 O) HELIX 1 AA1 ASP A 79 ASP A 96 1 18 HELIX 2 AA2 SER A 111 TYR A 119 1 9 HELIX 3 AA3 SER A 168 HIS A 170 5 3 HELIX 4 AA4 ASN A 176 LYS A 183 1 8 HELIX 5 AA5 GLU A 231 GLN A 236 1 6 HELIX 6 AA6 GLN A 236 ASN A 244 1 9 HELIX 7 AA7 ASN A 244 GLU A 267 1 24 HELIX 8 AA8 THR A 307 GLY A 317 1 11 HELIX 9 AA9 ASP A 353 GLY A 374 1 22 HELIX 10 AB1 ILE A 403 ASN A 412 1 10 HELIX 11 AB2 SER A 421 HIS A 435 1 15 HELIX 12 AB3 THR A 444 ILE A 457 1 14 HELIX 13 AB4 ASP A 510 GLN A 514 5 5 HELIX 14 AB5 SER A 537 GLU A 544 1 8 HELIX 15 AB6 ILE A 557 THR A 565 1 9 HELIX 16 AB7 SER A 569 VAL A 573 5 5 HELIX 17 AB8 ASP B 79 LYS B 97 1 19 HELIX 18 AB9 SER B 111 LYS B 120 1 10 HELIX 19 AC1 ASN B 176 LYS B 183 1 8 HELIX 20 AC2 MET B 223 LEU B 227 5 5 HELIX 21 AC3 GLU B 231 GLN B 236 1 6 HELIX 22 AC4 GLN B 236 ASN B 244 1 9 HELIX 23 AC5 ASN B 244 ARG B 268 1 25 HELIX 24 AC6 THR B 307 GLY B 317 1 11 HELIX 25 AC7 ASP B 353 GLY B 374 1 22 HELIX 26 AC8 ILE B 403 ASN B 412 1 10 HELIX 27 AC9 SER B 421 LYS B 436 1 16 HELIX 28 AD1 THR B 444 ILE B 457 1 14 HELIX 29 AD2 PRO B 472 SER B 476 5 5 HELIX 30 AD3 SER B 537 GLU B 544 1 8 HELIX 31 AD4 ILE B 557 THR B 565 1 9 HELIX 32 AD5 SER B 569 ILE B 574 5 6 SHEET 1 AA1 6 LEU A 133 SER A 143 0 SHEET 2 AA1 6 LEU A 149 GLY A 156 -1 O ASP A 153 N MET A 140 SHEET 3 AA1 6 GLU A 159 ASN A 166 -1 O VAL A 163 N PHE A 152 SHEET 4 AA1 6 LEU A 204 SER A 215 1 O ILE A 206 N GLN A 162 SHEET 5 AA1 6 ILE A 189 LYS A 198 -1 N GLY A 197 O SER A 205 SHEET 6 AA1 6 LEU A 133 SER A 143 -1 N ILE A 135 O ILE A 192 SHEET 1 AA2 8 PHE A 271 GLU A 272 0 SHEET 2 AA2 8 LYS A 321 PHE A 329 1 O TYR A 323 N PHE A 271 SHEET 3 AA2 8 GLU A 341 ALA A 350 -1 O SER A 344 N GLY A 326 SHEET 4 AA2 8 THR A 550 GLY A 556 -1 O GLY A 551 N TRP A 349 SHEET 5 AA2 8 LYS A 499 THR A 506 -1 N ASN A 503 O GLY A 554 SHEET 6 AA2 8 LEU A 492 ILE A 496 -1 N MET A 494 O VAL A 501 SHEET 7 AA2 8 PHE A 466 VAL A 469 -1 N PHE A 466 O PHE A 495 SHEET 8 AA2 8 LYS A 400 SER A 402 1 N VAL A 401 O VAL A 469 SHEET 1 AA3 3 MET A 278 ASN A 279 0 SHEET 2 AA3 3 LEU A 299 LEU A 303 -1 O TYR A 302 N ASN A 279 SHEET 3 AA3 3 ILE A 291 HIS A 294 -1 N HIS A 294 O LEU A 299 SHEET 1 AA4 2 LYS A 377 TYR A 380 0 SHEET 2 AA4 2 ILE A 390 ASP A 393 -1 O ILE A 390 N TYR A 380 SHEET 1 AA5 6 LEU B 133 SER B 143 0 SHEET 2 AA5 6 LEU B 149 GLY B 156 -1 O VAL B 155 N ARG B 138 SHEET 3 AA5 6 GLU B 159 ASN B 166 -1 O ALA B 165 N ARG B 150 SHEET 4 AA5 6 LEU B 204 SER B 215 1 O ILE B 206 N GLN B 162 SHEET 5 AA5 6 ILE B 189 LYS B 198 -1 N ILE B 189 O LEU B 214 SHEET 6 AA5 6 LEU B 133 SER B 143 -1 N ILE B 135 O ILE B 192 SHEET 1 AA6 8 PHE B 271 GLU B 272 0 SHEET 2 AA6 8 LYS B 321 PHE B 329 1 O TYR B 323 N PHE B 271 SHEET 3 AA6 8 GLU B 341 ALA B 350 -1 O SER B 344 N GLY B 326 SHEET 4 AA6 8 THR B 550 GLY B 556 -1 O GLY B 551 N TRP B 349 SHEET 5 AA6 8 LYS B 499 THR B 506 -1 N ASN B 503 O GLY B 554 SHEET 6 AA6 8 ARG B 491 ILE B 496 -1 N LEU B 492 O ALA B 504 SHEET 7 AA6 8 PHE B 466 VAL B 469 -1 N ILE B 468 O GLU B 493 SHEET 8 AA6 8 LYS B 400 SER B 402 1 N VAL B 401 O PHE B 467 SHEET 1 AA7 3 MET B 278 ASN B 279 0 SHEET 2 AA7 3 LEU B 299 LEU B 303 -1 O TYR B 302 N ASN B 279 SHEET 3 AA7 3 ILE B 291 HIS B 294 -1 N THR B 292 O LEU B 301 SHEET 1 AA8 2 LYS B 377 TYR B 380 0 SHEET 2 AA8 2 ILE B 390 ASP B 393 -1 O ILE B 392 N ILE B 378 SSBOND 1 CYS A 517 CYS A 540 1555 1555 2.04 SSBOND 2 CYS B 517 CYS B 540 1555 1555 2.03 CISPEP 1 PRO A 396 PRO A 397 0 -2.17 CISPEP 2 ASN A 441 PRO A 442 0 -4.73 CISPEP 3 PRO B 396 PRO B 397 0 0.89 CISPEP 4 ASN B 441 PRO B 442 0 5.98 CRYST1 71.916 95.551 168.253 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013905 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005943 0.00000