HEADER TRANSFERASE 19-JUL-17 5WIM TITLE JAK2 PSEUDOKINASE IN COMPLEX WITH AT9283 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE JAK2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 536-812; COMPND 5 SYNONYM: JANUS KINASE 2,JAK-2; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: JAK2; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS JAK2, PSEUDOKINASE, AT9283, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.LI,M.J.ECK,K.LI,E.PARK REVDAT 4 13-MAR-24 5WIM 1 REMARK REVDAT 3 01-MAY-19 5WIM 1 JRNL REVDAT 2 20-MAR-19 5WIM 1 JRNL REVDAT 1 01-AUG-18 5WIM 0 JRNL AUTH R.MCNALLY,Q.LI,K.LI,C.DEKKER,E.VANGREVELINGHE,M.JONES, JRNL AUTH 2 P.CHENE,R.MACHAUER,T.RADIMERSKI,M.J.ECK JRNL TITL DISCOVERY AND STRUCTURAL CHARACTERIZATION OF ATP-SITE JRNL TITL 2 LIGANDS FOR THE WILD-TYPE AND V617F MUTANT JAK2 PSEUDOKINASE JRNL TITL 3 DOMAIN. JRNL REF ACS CHEM. BIOL. V. 14 587 2019 JRNL REFN ESSN 1554-8937 JRNL PMID 30763067 JRNL DOI 10.1021/ACSCHEMBIO.8B00722 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10723 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 507 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 48.5742 - 4.0475 1.00 2665 133 0.1817 0.2164 REMARK 3 2 4.0475 - 3.2128 1.00 2529 134 0.2030 0.2393 REMARK 3 3 3.2128 - 2.8068 1.00 2520 125 0.2412 0.3353 REMARK 3 4 2.8068 - 2.5502 1.00 2502 115 0.2725 0.3542 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.60 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 : 0.008 2286 REMARK 3 ANGLE : 1.083 3092 REMARK 3 CHIRALITY : 0.047 338 REMARK 3 PLANARITY : 0.007 397 REMARK 3 DIHEDRAL : 18.377 1378 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5WIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000229052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10739 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : 0.12300 REMARK 200 FOR THE DATA SET : 14.3000 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) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.72900 REMARK 200 R SYM FOR SHELL (I) : 0.87800 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM ACETATE, 100 MM TRIS REMARK 280 -HCL, 18%-30%(W/V) POLYETHYLENE GLYCOL 4000., PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 28.89550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.34350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.89550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.34350 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 THR A 810 REMARK 465 PRO A 811 REMARK 465 ASP A 812 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 ASN A 548 -136.78 -107.31 REMARK 500 CYS A 618 -84.18 -119.23 REMARK 500 ASP A 635 -70.05 -40.90 REMARK 500 ASN A 673 49.46 -155.86 REMARK 500 ASP A 686 77.27 58.42 REMARK 500 ASP A 699 151.14 -38.24 REMARK 500 ALA A 777 95.90 -54.50 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 35R A 901 DBREF 5WIM A 536 812 UNP O60674 JAK2_HUMAN 536 812 SEQADV 5WIM ALA A 659 UNP O60674 TRP 659 ENGINEERED MUTATION SEQADV 5WIM ALA A 777 UNP O60674 TRP 777 ENGINEERED MUTATION SEQADV 5WIM HIS A 794 UNP O60674 PHE 794 ENGINEERED MUTATION SEQRES 1 A 277 VAL PHE HIS LYS ILE ARG ASN GLU ASP LEU ILE PHE ASN SEQRES 2 A 277 GLU SER LEU GLY GLN GLY THR PHE THR LYS ILE PHE LYS SEQRES 3 A 277 GLY VAL ARG ARG GLU VAL GLY ASP TYR GLY GLN LEU HIS SEQRES 4 A 277 GLU THR GLU VAL LEU LEU LYS VAL LEU ASP LYS ALA HIS SEQRES 5 A 277 ARG ASN TYR SER GLU SER PHE PHE GLU ALA ALA SER MET SEQRES 6 A 277 MET SER LYS LEU SER HIS LYS HIS LEU VAL LEU ASN TYR SEQRES 7 A 277 GLY VAL CYS VAL CYS GLY ASP GLU ASN ILE LEU VAL GLN SEQRES 8 A 277 GLU PHE VAL LYS PHE GLY SER LEU ASP THR TYR LEU LYS SEQRES 9 A 277 LYS ASN LYS ASN CYS ILE ASN ILE LEU TRP LYS LEU GLU SEQRES 10 A 277 VAL ALA LYS GLN LEU ALA ALA ALA MET HIS PHE LEU GLU SEQRES 11 A 277 GLU ASN THR LEU ILE HIS GLY ASN VAL CYS ALA LYS ASN SEQRES 12 A 277 ILE LEU LEU ILE ARG GLU GLU ASP ARG LYS THR GLY ASN SEQRES 13 A 277 PRO PRO PHE ILE LYS LEU SER ASP PRO GLY ILE SER ILE SEQRES 14 A 277 THR VAL LEU PRO LYS ASP ILE LEU GLN GLU ARG ILE PRO SEQRES 15 A 277 TRP VAL PRO PRO GLU CYS ILE GLU ASN PRO LYS ASN LEU SEQRES 16 A 277 ASN LEU ALA THR ASP LYS TRP SER PHE GLY THR THR LEU SEQRES 17 A 277 TRP GLU ILE CYS SER GLY GLY ASP LYS PRO LEU SER ALA SEQRES 18 A 277 LEU ASP SER GLN ARG LYS LEU GLN PHE TYR GLU ASP ARG SEQRES 19 A 277 HIS GLN LEU PRO ALA PRO LYS ALA ALA GLU LEU ALA ASN SEQRES 20 A 277 LEU ILE ASN ASN CYS MET ASP TYR GLU PRO ASP HIS ARG SEQRES 21 A 277 PRO SER PHE ARG ALA ILE ILE ARG ASP LEU ASN SER LEU SEQRES 22 A 277 PHE THR PRO ASP HET 35R A 901 28 HETNAM 35R 1-CYCLOPROPYL-3-{3-[5-(MORPHOLIN-4-YLMETHYL)-1H- HETNAM 2 35R BENZIMIDAZOL-2-YL]-1H-PYRAZOL-4-YL}UREA FORMUL 2 35R C19 H23 N7 O2 FORMUL 3 HOH *22(H2 O) HELIX 1 AA1 ASP A 569 GLY A 571 5 3 HELIX 2 AA2 HIS A 587 ASN A 589 5 3 HELIX 3 AA3 TYR A 590 LEU A 604 1 15 HELIX 4 AA4 SER A 633 ASN A 641 1 9 HELIX 5 AA5 ASN A 646 ASN A 667 1 22 HELIX 6 AA6 CYS A 675 LYS A 677 5 3 HELIX 7 AA7 PRO A 708 ARG A 715 1 8 HELIX 8 AA8 PRO A 720 ASN A 726 1 7 HELIX 9 AA9 PRO A 727 ASN A 731 5 5 HELIX 10 AB1 LEU A 732 SER A 748 1 17 HELIX 11 AB2 ASP A 758 ASP A 768 1 11 HELIX 12 AB3 LEU A 780 MET A 788 1 9 HELIX 13 AB4 GLU A 791 ARG A 795 5 5 HELIX 14 AB5 SER A 797 SER A 807 1 11 SHEET 1 AA1 6 LYS A 539 ARG A 541 0 SHEET 2 AA1 6 ASN A 612 VAL A 617 1 O VAL A 615 N ILE A 540 SHEET 3 AA1 6 ILE A 623 GLU A 627 -1 O VAL A 625 N TYR A 613 SHEET 4 AA1 6 LEU A 573 LEU A 583 -1 N LEU A 579 O GLN A 626 SHEET 5 AA1 6 THR A 557 VAL A 567 -1 N GLU A 566 O HIS A 574 SHEET 6 AA1 6 LEU A 545 GLY A 554 -1 N ASN A 548 O LYS A 561 SHEET 1 AA2 2 ILE A 679 ARG A 683 0 SHEET 2 AA2 2 PHE A 694 LEU A 697 -1 O LYS A 696 N LEU A 680 CISPEP 1 ILE A 716 PRO A 717 0 4.72 SITE 1 AC1 12 LEU A 551 LEU A 579 LYS A 581 GLU A 627 SITE 2 AC1 12 VAL A 629 LYS A 630 PHE A 631 GLY A 632 SITE 3 AC1 12 LYS A 677 ASN A 678 LEU A 680 SER A 698 CRYST1 57.791 60.687 89.600 90.00 90.00 90.00 P 21 21 21 4 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 0.017304 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011161 0.00000