PDB Short entry for 5NK0 HEADER TRANSFERASE 31-MAR-17 5NK0 TITLE CRYSTAL STRUCTURE OF EPHRIN A2 (EPHA2) RECEPTOR PROTEIN KINASE WITH TITLE 2 COMPOUND 1J 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_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS INHIBITOR, COMPLEX, PROTEIN TYROSINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.KUDLINZKI,V.L.LINHARD,K.WITT,S.L.GANDE,K.SAXENA,S.HEINZLMEIR, AUTHOR 2 G.MEDARD,B.KUESTER,H.SCHWALBE REVDAT 5 17-JAN-24 5NK0 1 REMARK REVDAT 4 14-AUG-19 5NK0 1 REMARK REVDAT 3 12-JUN-19 5NK0 1 AUTHOR REVDAT 2 28-JUN-17 5NK0 1 JRNL REVDAT 1 07-JUN-17 5NK0 0 JRNL AUTH S.HEINZLMEIR,J.LOHSE,T.TREIBER,D.KUDLINZKI,V.LINHARD, JRNL AUTH 2 S.L.GANDE,S.SREERAMULU,K.SAXENA,X.LIU,M.WILHELM,H.SCHWALBE, JRNL AUTH 3 B.KUSTER,G.MEDARD JRNL TITL CHEMOPROTEOMICS-AIDED MEDICINAL CHEMISTRY FOR THE DISCOVERY JRNL TITL 2 OF EPHA2 INHIBITORS. JRNL REF CHEMMEDCHEM V. 12 999 2017 JRNL REFN ESSN 1860-7187 JRNL PMID 28544567 JRNL DOI 10.1002/CMDC.201700217 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 33701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1685 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 39.1480 - 3.6550 1.00 2763 146 0.1509 0.1646 REMARK 3 2 3.6550 - 2.9013 0.99 2712 143 0.1456 0.1757 REMARK 3 3 2.9013 - 2.5347 0.99 2721 143 0.1592 0.1885 REMARK 3 4 2.5347 - 2.3030 0.99 2654 140 0.1585 0.2012 REMARK 3 5 2.3030 - 2.1379 0.98 2700 142 0.1575 0.1875 REMARK 3 6 2.1379 - 2.0119 0.98 2677 140 0.1568 0.1910 REMARK 3 7 2.0119 - 1.9111 0.97 2662 141 0.1637 0.2345 REMARK 3 8 1.9111 - 1.8279 0.97 2648 139 0.1827 0.2358 REMARK 3 9 1.8279 - 1.7576 0.97 2665 140 0.1984 0.2032 REMARK 3 10 1.7576 - 1.6969 0.97 2595 137 0.2136 0.2566 REMARK 3 11 1.6969 - 1.6438 0.97 2656 140 0.2310 0.2814 REMARK 3 12 1.6438 - 1.5969 0.94 2563 134 0.2544 0.2832 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.90 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 : 0.007 2328 REMARK 3 ANGLE : 1.075 3145 REMARK 3 CHIRALITY : 0.054 334 REMARK 3 PLANARITY : 0.005 395 REMARK 3 DIHEDRAL : 14.571 1420 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 5NK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS XDSAPP 2.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.597 REMARK 200 RESOLUTION RANGE LOW (A) : 39.136 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.950 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.820 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: 5I9U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37.5% MPD/PEG1000/PEG3350 (MD), 0.175 REMARK 280 M AMINO ACIDS MIX (MD), 0.1 M BUFFER SYSTEM 3 (MD) PH8.5, 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 52.41900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 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 ILE A 779 REMARK 465 ARG A 890 REMARK 465 LEU A 895 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 ARG A 738 -13.41 73.85 REMARK 500 SER A 756 -35.90 -130.11 REMARK 500 TRP A 819 -122.10 50.64 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 91E A 1001 DBREF 5NK0 A 596 900 UNP P29317 EPHA2_HUMAN 596 900 SEQADV 5NK0 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 91E A1001 64 HETNAM 91E 2-[[3-[(3-AZANYL-2,2-DIMETHYL-PROPYL) HETNAM 2 91E CARBAMOYL]PHENYL]AMINO]-~{N}-(2-CHLORANYL-6-METHYL- HETNAM 3 91E PHENYL)-1,3-THIAZOLE-5-CARBOXAMIDE FORMUL 2 91E C23 H26 CL N5 O2 S FORMUL 3 HOH *175(H2 O) HELIX 1 AA1 HIS A 609 SER A 611 5 3 HELIX 2 AA2 THR A 653 GLY A 668 1 16 HELIX 3 AA3 LEU A 700 GLU A 706 1 7 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 THR A 883 5 6 SHEET 1 AA1 5 VAL A 613 ALA A 621 0 SHEET 2 AA1 5 GLU A 626 THR A 634 -1 O VAL A 627 N GLY A 620 SHEET 3 AA1 5 LYS A 639 LEU A 648 -1 O LYS A 639 N THR A 634 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 GLY A 680 O ILE A 691 SHEET 1 AA2 3 GLY A 698 ALA A 699 0 SHEET 2 AA2 3 ILE A 745 VAL A 747 -1 O VAL A 747 N GLY A 698 SHEET 3 AA2 3 CYS A 753 VAL A 755 -1 O LYS A 754 N LEU A 746 CISPEP 1 LYS A 686 PRO A 687 0 0.28 SITE 1 AC1 14 ALA A 644 LYS A 646 GLU A 663 ILE A 676 SITE 2 AC1 14 ILE A 690 THR A 692 GLU A 693 TYR A 694 SITE 3 AC1 14 MET A 695 GLU A 696 GLY A 698 LEU A 746 SITE 4 AC1 14 SER A 756 HOH A1181 CRYST1 32.318 104.838 39.259 90.00 94.53 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 0.030943 0.000000 0.002452 0.00000 SCALE2 0.000000 0.009539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025552 0.00000