HEADER TRANSFERASE 10-NOV-22 8BM8 TITLE CRYSTAL STRUCTURE OF EPHRIN A2 (EPHA2) RECEPTOR PROTEIN KINASE WITH TITLE 2 COMPOUND 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-A RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EPITHELIAL CELL KINASE,TYROSINE-PROTEIN KINASE RECEPTOR ECK; COMPND 5 EC: 2.7.10.1; COMPND 6 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: EPHA2, ECK; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS INHIBITOR, COMPLEX, PROTEIN TYROSINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.LINHARD,K.WITT,S.GANDE,J.WOLLENHAUPT,F.LENNARTZ,M.S.WEISS, AUTHOR 2 H.SCHWALBE REVDAT 1 05-JUN-24 8BM8 0 JRNL AUTH A.TROESTER JRNL TITL (PLACEHOLDER, WILL BE FILLED AFTER PUBLICATION) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.68 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 28696 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) : 0.190 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1434 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 38.1800 - 3.6100 0.96 2740 144 0.1576 0.1652 REMARK 3 2 3.6100 - 2.8700 0.98 2773 146 0.1666 0.2115 REMARK 3 3 2.8700 - 2.5100 0.98 2768 145 0.1739 0.2307 REMARK 3 4 2.5100 - 2.2800 0.97 2742 145 0.1834 0.2400 REMARK 3 5 2.2800 - 2.1100 0.98 2749 145 0.1916 0.2407 REMARK 3 6 2.1100 - 1.9900 0.98 2753 144 0.2048 0.2422 REMARK 3 7 1.9900 - 1.8900 0.97 2743 145 0.2289 0.2661 REMARK 3 8 1.8900 - 1.8100 0.97 2691 142 0.2440 0.2694 REMARK 3 9 1.8100 - 1.7400 0.96 2713 142 0.2932 0.3347 REMARK 3 10 1.7400 - 1.6800 0.91 2590 136 0.3539 0.4074 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) : 0.263 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.45 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 : 0.007 2427 REMARK 3 ANGLE : 0.989 3298 REMARK 3 CHIRALITY : 0.053 342 REMARK 3 PLANARITY : 0.013 507 REMARK 3 DIHEDRAL : 7.323 400 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 605:895) REMARK 3 ORIGIN FOR THE GROUP (A): -81.5073 -8.0927 90.1443 REMARK 3 T TENSOR REMARK 3 T11: 0.1049 T22: 0.2299 REMARK 3 T33: 0.1228 T12: 0.0096 REMARK 3 T13: -0.0056 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.4755 L22: 1.1872 REMARK 3 L33: 0.3363 L12: 0.2455 REMARK 3 L13: 0.0122 L23: -0.0818 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: -0.0226 S13: -0.0490 REMARK 3 S21: -0.0182 S22: 0.0248 S23: -0.0529 REMARK 3 S31: 0.0337 S32: 0.0324 S33: -0.0197 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 8BM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28709 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 38.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.320 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.17 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6Q7D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37,5 % MPD_PEG1000_PEG3350, 100 MM REMARK 280 MORPHEUS AMINO ACIDS MIX, 100 MM BIS-TRIS PH 6.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 53.21500 REMARK 290 SMTRY3 2 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 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 GLY A 595 REMARK 465 ASP A 596 REMARK 465 PRO A 597 REMARK 465 ASN A 598 REMARK 465 GLN A 599 REMARK 465 ALA A 600 REMARK 465 VAL A 601 REMARK 465 LEU A 602 REMARK 465 LYS A 603 REMARK 465 PHE A 604 REMARK 465 THR A 634 REMARK 465 SER A 635 REMARK 465 SER A 636 REMARK 465 GLY A 637 REMARK 465 LYS A 638 REMARK 465 SER A 761 REMARK 465 ARG A 762 REMARK 465 VAL A 763 REMARK 465 LEU A 764 REMARK 465 GLU A 765 REMARK 465 ASP A 766 REMARK 465 ASP A 767 REMARK 465 PRO A 768 REMARK 465 GLU A 769 REMARK 465 ALA A 770 REMARK 465 THR A 771 REMARK 465 TYR A 772 REMARK 465 THR A 773 REMARK 465 THR A 774 REMARK 465 SER A 775 REMARK 465 GLY A 776 REMARK 465 GLY A 777 REMARK 465 LYS A 778 REMARK 465 PRO A 896 REMARK 465 SER A 897 REMARK 465 THR A 898 REMARK 465 SER A 899 REMARK 465 GLY A 900 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 PHE A 624 68.67 -159.00 REMARK 500 ARG A 738 -13.39 79.39 REMARK 500 TYR A 791 23.59 -146.99 REMARK 500 TRP A 819 -124.61 46.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BM8 A 596 900 UNP P29317 EPHA2_HUMAN 596 900 SEQADV 8BM8 GLY A 595 UNP P29317 EXPRESSION TAG SEQRES 1 A 306 GLY ASP PRO ASN GLN ALA VAL LEU LYS PHE THR THR GLU SEQRES 2 A 306 ILE HIS PRO SER CYS VAL THR ARG GLN LYS VAL ILE GLY SEQRES 3 A 306 ALA GLY GLU PHE GLY GLU VAL TYR LYS GLY MET LEU LYS SEQRES 4 A 306 THR SER SER GLY LYS LYS GLU VAL PRO VAL ALA ILE LYS SEQRES 5 A 306 THR LEU LYS ALA GLY TYR THR GLU LYS GLN ARG VAL ASP SEQRES 6 A 306 PHE LEU GLY GLU ALA GLY ILE MET GLY GLN PHE SER HIS SEQRES 7 A 306 HIS ASN ILE ILE ARG LEU GLU GLY VAL ILE SER LYS TYR SEQRES 8 A 306 LYS PRO MET MET ILE ILE THR GLU TYR MET GLU ASN GLY SEQRES 9 A 306 ALA LEU ASP LYS PHE LEU ARG GLU LYS ASP GLY GLU PHE SEQRES 10 A 306 SER VAL LEU GLN LEU VAL GLY MET LEU ARG GLY ILE ALA SEQRES 11 A 306 ALA GLY MET LYS TYR LEU ALA ASN MET ASN TYR VAL HIS SEQRES 12 A 306 ARG ASP LEU ALA ALA ARG ASN ILE LEU VAL ASN SER ASN SEQRES 13 A 306 LEU VAL CYS LYS VAL SER ASP PHE GLY LEU SER ARG VAL SEQRES 14 A 306 LEU GLU ASP ASP PRO GLU ALA THR TYR THR THR SER GLY SEQRES 15 A 306 GLY LYS ILE PRO ILE ARG TRP THR ALA PRO GLU ALA ILE SEQRES 16 A 306 SER TYR ARG LYS PHE THR SER ALA SER ASP VAL TRP SER SEQRES 17 A 306 PHE GLY ILE VAL MET TRP GLU VAL MET THR TYR GLY GLU SEQRES 18 A 306 ARG PRO TYR TRP GLU LEU SER ASN HIS GLU VAL MET LYS SEQRES 19 A 306 ALA ILE ASN ASP GLY PHE ARG LEU PRO THR PRO MET ASP SEQRES 20 A 306 CYS PRO SER ALA ILE TYR GLN LEU MET MET GLN CYS TRP SEQRES 21 A 306 GLN GLN GLU ARG ALA ARG ARG PRO LYS PHE ALA ASP ILE SEQRES 22 A 306 VAL SER ILE LEU ASP LYS LEU ILE ARG ALA PRO ASP SER SEQRES 23 A 306 LEU LYS THR LEU ALA ASP PHE ASP PRO ARG VAL SER ILE SEQRES 24 A 306 ARG LEU PRO SER THR SER GLY HET QT1 A1001 70 HETNAM QT1 ~{N}-(3-CYANOPHENYL)-4-METHYL-3-[(1-METHYL-6-PYRIDIN-3- HETNAM 2 QT1 YL-PYRAZOLO[3,4-D]PYRIMIDIN-4-YL)AMINO]BENZAMIDE FORMUL 2 QT1 C26 H20 N8 O FORMUL 3 HOH *102(H2 O) HELIX 1 AA1 HIS A 609 SER A 611 5 3 HELIX 2 AA2 THR A 653 PHE A 670 1 18 HELIX 3 AA3 ALA A 699 LYS A 707 1 9 HELIX 4 AA4 SER A 712 MET A 733 1 22 HELIX 5 AA5 ALA A 741 ARG A 743 5 3 HELIX 6 AA6 PRO A 780 THR A 784 5 5 HELIX 7 AA7 ALA A 785 ARG A 792 1 8 HELIX 8 AA8 THR A 795 THR A 812 1 18 HELIX 9 AA9 SER A 822 ASP A 832 1 11 HELIX 10 AB1 PRO A 843 TRP A 854 1 12 HELIX 11 AB2 GLU A 857 ARG A 861 5 5 HELIX 12 AB3 LYS A 863 ALA A 877 1 15 HELIX 13 AB4 PRO A 878 LYS A 882 5 5 SHEET 1 AA1 5 VAL A 613 ALA A 621 0 SHEET 2 AA1 5 GLU A 626 LEU A 632 -1 O VAL A 627 N ILE A 619 SHEET 3 AA1 5 VAL A 641 LEU A 648 -1 O ILE A 645 N TYR A 628 SHEET 4 AA1 5 MET A 688 GLU A 693 -1 O ILE A 690 N LYS A 646 SHEET 5 AA1 5 LEU A 678 ILE A 682 -1 N GLU A 679 O ILE A 691 SHEET 1 AA2 2 ILE A 745 VAL A 747 0 SHEET 2 AA2 2 CYS A 753 VAL A 755 -1 O LYS A 754 N LEU A 746 CISPEP 1 LYS A 686 PRO A 687 0 -5.78 CRYST1 32.540 106.430 40.250 90.00 108.44 90.00 P 1 21 1 2 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 0.030731 0.000000 0.010247 0.00000 SCALE2 0.000000 0.009396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026189 0.00000