HEADER TRANSFERASE 19-JUL-17 5WIJ TITLE JAK2 PSEUDOKINASE IN COMPLEX WITH NU6140 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, NU6140, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.LI,M.J.ECK,K.LI,E.PARK REVDAT 4 13-MAR-24 5WIJ 1 REMARK REVDAT 3 01-MAY-19 5WIJ 1 JRNL REVDAT 2 20-MAR-19 5WIJ 1 JRNL REVDAT 1 01-AUG-18 5WIJ 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. 2.04 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1036 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 30.7170 - 3.9001 0.99 2997 135 0.1697 0.1700 REMARK 3 2 3.9001 - 3.0966 1.00 2811 176 0.1949 0.2147 REMARK 3 3 3.0966 - 2.7054 1.00 2843 128 0.2355 0.2794 REMARK 3 4 2.7054 - 2.4582 1.00 2804 138 0.2286 0.2649 REMARK 3 5 2.4582 - 2.2820 1.00 2777 155 0.2469 0.2977 REMARK 3 6 2.2820 - 2.1475 1.00 2778 136 0.2757 0.3331 REMARK 3 7 2.1475 - 2.0400 1.00 2754 168 0.3262 0.3453 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.26 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 : 0.002 2281 REMARK 3 ANGLE : 0.546 3084 REMARK 3 CHIRALITY : 0.042 337 REMARK 3 PLANARITY : 0.003 396 REMARK 3 DIHEDRAL : 15.685 1377 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 5WIJ 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_1000229093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20816 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 30.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62900 REMARK 200 R SYM FOR SHELL (I) : 0.77600 REMARK 200 FOR SHELL : 2.400 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 (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 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 28.71150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.28050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.48050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.28050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.71150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.48050 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 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 PHE A 809 CG CD1 CD2 CE1 CE2 CZ 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 O HOH A 1100 O HOH A 1101 1.84 REMARK 500 O HOH A 1047 O HOH A 1086 1.91 REMARK 500 O HOH A 1082 O HOH A 1088 1.93 REMARK 500 O HOH A 1019 O HOH A 1041 2.17 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 ASN A 548 -135.82 -117.02 REMARK 500 ASN A 641 45.20 -102.47 REMARK 500 CYS A 644 35.98 -95.01 REMARK 500 ASN A 673 56.24 -151.01 REMARK 500 ASN A 726 109.71 -160.95 REMARK 500 ALA A 777 92.48 -68.93 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 AQG A 901 DBREF 5WIJ A 536 812 UNP O60674 JAK2_HUMAN 536 812 SEQADV 5WIJ ALA A 659 UNP O60674 TRP 659 ENGINEERED MUTATION SEQADV 5WIJ ALA A 777 UNP O60674 TRP 777 ENGINEERED MUTATION SEQADV 5WIJ 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 AQG A 901 31 HETNAM AQG 4-{[6-(CYCLOHEXYLMETHOXY)-7H-PURIN-2-YL]AMINO}-N,N- HETNAM 2 AQG DIETHYLBENZAMIDE FORMUL 2 AQG C23 H30 N6 O2 FORMUL 3 HOH *101(H2 O) HELIX 1 AA1 ASP A 569 GLY A 571 5 3 HELIX 2 AA2 LYS A 585 ASN A 589 5 5 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 LEU A 730 5 4 HELIX 10 AB1 ASN A 731 SER A 748 1 18 HELIX 11 AB2 ASP A 758 ASP A 768 1 11 HELIX 12 AB3 ALA A 777 GLU A 779 5 3 HELIX 13 AB4 LEU A 780 MET A 788 1 9 HELIX 14 AB5 GLU A 791 ARG A 795 5 5 HELIX 15 AB6 SER A 797 ASN A 806 1 10 HELIX 16 AB7 SER A 807 PHE A 809 5 3 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 GLY A 614 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 ARG A 564 O THR A 576 SHEET 6 AA1 6 LEU A 545 GLY A 554 -1 N GLU A 549 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 4.48 SITE 1 AC1 12 LEU A 551 GLY A 552 ILE A 559 LEU A 579 SITE 2 AC1 12 GLN A 626 GLU A 627 PHE A 628 VAL A 629 SITE 3 AC1 12 LYS A 630 GLY A 632 LEU A 680 HOH A1047 CRYST1 57.423 60.961 90.561 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 0.017415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016404 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011042 0.00000