HEADER TRANSFERASE 15-NOV-22 8BOF TITLE CRYSTAL STRUCTURE OF EPHRIN A2 (EPHA2) RECEPTOR PROTEIN KINASE WITH TITLE 2 COMPOUND 12 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 6 07-FEB-24 8BOF 1 REMARK REVDAT 5 03-MAY-23 8BOF 1 JRNL REVDAT 4 05-APR-23 8BOF 1 JRNL REVDAT 3 22-MAR-23 8BOF 1 JRNL REVDAT 2 15-MAR-23 8BOF 1 JRNL REVDAT 1 08-MAR-23 8BOF 0 JRNL AUTH A.TROSTER,M.DIPRIMA,N.JORES,D.KUDLINZKI,S.SREERAMULU, JRNL AUTH 2 S.L.GANDE,V.LINHARD,D.LUDIG,A.SCHUG,K.SAXENA,M.REINECKE, JRNL AUTH 3 S.HEINZLMEIR,M.S.LEISEGANG,J.WOLLENHAUPT,F.LENNARTZ, JRNL AUTH 4 M.S.WEISS,B.KUSTER,G.TOSATO,H.SCHWALBE JRNL TITL OPTIMIZATION OF THE LEAD COMPOUND NVP-BHG712 AS A COLORECTAL JRNL TITL 2 CANCER INHIBITOR. JRNL REF CHEMISTRY V. 29 03967 2023 JRNL REFN ISSN 0947-6539 JRNL PMID 36799129 JRNL DOI 10.1002/CHEM.202203967 REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 23199 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1161 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 31.0300 - 3.6300 0.99 2787 147 0.1508 0.1635 REMARK 3 2 3.6300 - 2.8800 1.00 2795 147 0.1642 0.2094 REMARK 3 3 2.8800 - 2.5200 0.99 2742 145 0.1820 0.2268 REMARK 3 4 2.5200 - 2.2900 1.00 2800 147 0.1846 0.2207 REMARK 3 5 2.2900 - 2.1200 0.99 2727 144 0.2050 0.2265 REMARK 3 6 2.1200 - 2.0000 0.99 2778 146 0.2374 0.2834 REMARK 3 7 2.0000 - 1.9000 0.99 2746 145 0.2752 0.3080 REMARK 3 8 1.9000 - 1.8200 0.96 2663 140 0.2946 0.3438 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) : 0.252 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.83 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 : 0.018 2265 REMARK 3 ANGLE : 1.268 3065 REMARK 3 CHIRALITY : 0.074 328 REMARK 3 PLANARITY : 0.017 429 REMARK 3 DIHEDRAL : 12.913 881 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 605 THROUGH 640 ) REMARK 3 ORIGIN FOR THE GROUP (A): -83.0619 -29.2842 81.1249 REMARK 3 T TENSOR REMARK 3 T11: 0.3206 T22: 0.2206 REMARK 3 T33: 0.4350 T12: 0.0157 REMARK 3 T13: -0.0054 T23: -0.0925 REMARK 3 L TENSOR REMARK 3 L11: 6.4225 L22: 3.8988 REMARK 3 L33: 3.1912 L12: 2.0122 REMARK 3 L13: 0.1695 L23: -0.5915 REMARK 3 S TENSOR REMARK 3 S11: 0.0117 S12: -0.1106 S13: -0.0829 REMARK 3 S21: -0.1907 S22: 0.2166 S23: -0.5560 REMARK 3 S31: 0.0137 S32: 0.1887 S33: -0.2015 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 641 THROUGH 669 ) REMARK 3 ORIGIN FOR THE GROUP (A): -88.6597 -27.3128 91.2837 REMARK 3 T TENSOR REMARK 3 T11: 0.2473 T22: 0.1765 REMARK 3 T33: 0.2988 T12: 0.0080 REMARK 3 T13: -0.0411 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.9643 L22: 3.3941 REMARK 3 L33: 6.8060 L12: 0.5239 REMARK 3 L13: 0.2516 L23: -4.0838 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: -0.2107 S13: 0.1416 REMARK 3 S21: 0.2090 S22: 0.2448 S23: 0.2106 REMARK 3 S31: -0.1404 S32: 0.0588 S33: -0.1445 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 670 THROUGH 712 ) REMARK 3 ORIGIN FOR THE GROUP (A): -82.4343 -16.2975 82.3567 REMARK 3 T TENSOR REMARK 3 T11: 0.2063 T22: 0.2266 REMARK 3 T33: 0.1618 T12: -0.0017 REMARK 3 T13: 0.0086 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.5177 L22: 1.2783 REMARK 3 L33: 0.3128 L12: 0.2397 REMARK 3 L13: 0.2718 L23: 0.1401 REMARK 3 S TENSOR REMARK 3 S11: -0.0037 S12: 0.0753 S13: -0.1341 REMARK 3 S21: 0.0312 S22: 0.0498 S23: -0.0503 REMARK 3 S31: 0.1053 S32: 0.0522 S33: -0.0464 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 713 THROUGH 822 ) REMARK 3 ORIGIN FOR THE GROUP (A): -82.4130 -5.0751 92.9677 REMARK 3 T TENSOR REMARK 3 T11: 0.1357 T22: 0.1766 REMARK 3 T33: 0.1554 T12: 0.0003 REMARK 3 T13: 0.0008 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.5523 L22: 0.7838 REMARK 3 L33: 1.8475 L12: 0.0963 REMARK 3 L13: 0.0639 L23: 0.2095 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: -0.1015 S13: -0.0845 REMARK 3 S21: 0.0494 S22: 0.0024 S23: -0.0224 REMARK 3 S31: 0.1244 S32: 0.0415 S33: -0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 823 THROUGH 881 ) REMARK 3 ORIGIN FOR THE GROUP (A): -82.2206 6.2037 95.5182 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.1636 REMARK 3 T33: 0.1779 T12: 0.0126 REMARK 3 T13: -0.0008 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 1.9907 L22: 1.4462 REMARK 3 L33: 2.3490 L12: -0.1590 REMARK 3 L13: 0.5363 L23: -0.3915 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: -0.1662 S13: 0.0621 REMARK 3 S21: 0.0823 S22: -0.0267 S23: -0.0278 REMARK 3 S31: -0.0537 S32: -0.0055 S33: 0.0440 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 882 THROUGH 896 ) REMARK 3 ORIGIN FOR THE GROUP (A): -63.9028 14.8502 90.6785 REMARK 3 T TENSOR REMARK 3 T11: 0.2618 T22: 0.2552 REMARK 3 T33: 0.2913 T12: -0.0167 REMARK 3 T13: -0.0348 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 3.4661 L22: 1.2897 REMARK 3 L33: 3.9289 L12: -0.2349 REMARK 3 L13: 1.0529 L23: 0.0968 REMARK 3 S TENSOR REMARK 3 S11: -0.2567 S12: -0.5697 S13: 0.1520 REMARK 3 S21: 0.2018 S22: 0.1102 S23: -0.1940 REMARK 3 S31: 0.0086 S32: 0.4041 S33: 0.1245 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 8BOF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-20 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 : BESSY REMARK 200 BEAMLINE : 14.1 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.780 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.77 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.030 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 (%): 35.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37,5 % PRECIPITANT MIX 4 (25% (V/V) REMARK 280 HEXYLENE GLYCOL, 25% (W/V) POLY(ETHYLENE GLYCOL) 1000, 25% (W/V) REMARK 280 POLY(ETHYLENE GLYCOL) 3350), 0.1M BUFFER SYSTEM 3 PH 8.5 (1M REMARK 280 BICINE, 1M TRIZMA BASE), 0.275 M AMINO ACIDS MIX (0.2 M DL- REMARK 280 ALANINE,0.2M DL-GLUTAMIC ACID MONOHYDRATE, 0.2M DL-LYSINE REMARK 280 MONOHYDROCHLORIDE, 0.2M DL-SERINE, 0.2M GLYCINE), 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 LEU A 602 REMARK 465 LYS A 603 REMARK 465 PHE A 604 REMARK 465 SER A 635 REMARK 465 SER A 636 REMARK 465 GLY A 637 REMARK 465 LYS A 638 REMARK 465 LYS A 639 REMARK 465 GLY A 759 REMARK 465 LEU A 760 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 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: 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 OD1 ASP A 888 O HOH A 1101 1.97 REMARK 500 OD2 ASP A 757 O HOH A 1102 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1145 O HOH A 1183 1454 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 782 CB ARG A 782 CG -0.205 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 799 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES 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 GLN A 616 -61.71 -123.40 REMARK 500 ARG A 738 -16.43 79.68 REMARK 500 TYR A 791 23.25 -145.66 REMARK 500 TRP A 819 -126.65 48.85 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 861 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8BOF A 596 900 UNP P29317 EPHA2_HUMAN 596 900 SEQADV 8BOF 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 R3L A1001 57 HETNAM R3L 4-METHYL-~{N}-(3-METHYLPHENYL)-3-[(1-METHYL-6-PYRIDIN- HETNAM 2 R3L 3-YL-PYRAZOLO[3,4-D]PYRIMIDIN-4-YL)AMINO]BENZAMIDE FORMUL 2 R3L C26 H23 N7 O FORMUL 3 HOH *100(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 GLY A 833 1 12 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 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 GLY A 680 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 -0.23 CRYST1 32.580 106.430 40.300 90.00 108.61 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 0.030694 0.000000 0.010336 0.00000 SCALE2 0.000000 0.009396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026183 0.00000