HEADER TRANSFERASE 13-OCT-12 2YN8 TITLE EPHB4 KINASE DOMAIN INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 598-892; COMPND 5 SYNONYM: HEPATOMA TRANSMEMBRANE KINASE, TYROSINE-PROTEIN KINASE COMPND 6 TYRO11; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS TRANSFERASE, UNPHOSPHORYLATED EXPDTA X-RAY DIFFRACTION AUTHOR J.READ,C.A.BRASSINGTON,R.OVERMANN REVDAT 3 24-APR-19 2YN8 1 SOURCE REVDAT 2 04-APR-18 2YN8 1 REMARK REVDAT 1 23-OCT-13 2YN8 0 JRNL AUTH R.C.OVERMAN,I.GREEN,C.M.TRUMAN,J.A.READ,K.J.EMBREY, JRNL AUTH 2 M.S.B.MCALISTER,T.K.ATTWOOD JRNL TITL STABILITY AND SOLUBILITY ENGINEERING OF THE EPHB4 TYROSINE JRNL TITL 2 KINASE CATALYTIC DOMAIN USING A RATIONALLY DESIGNED JRNL TITL 3 SYNTHETIC LIBRARY. JRNL REF PROTEIN ENG.DES.SEL. V. 26 695 2013 JRNL REFN ISSN 1741-0126 JRNL PMID 23840071 JRNL DOI 10.1093/PROTEIN/GZT032 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 40600 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2041 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.05 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2780 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2157 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2656 REMARK 3 BIN R VALUE (WORKING SET) : 0.2141 REMARK 3 BIN FREE R VALUE : 0.2474 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.46 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 124 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4005 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 419 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.15970 REMARK 3 B22 (A**2) : -8.38510 REMARK 3 B33 (A**2) : 6.22540 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.33320 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.275 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.191 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.167 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.184 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.165 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4173 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5676 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1441 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 97 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 597 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4173 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 544 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5289 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.14 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.96 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 608-888 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7568 -1.8614 -20.6149 REMARK 3 T TENSOR REMARK 3 T11: -0.0293 T22: 0.0175 REMARK 3 T33: 0.0276 T12: -0.0052 REMARK 3 T13: -0.0083 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.6717 L22: 0.4075 REMARK 3 L33: 1.2035 L12: -0.1936 REMARK 3 L13: 0.2469 L23: -0.2164 REMARK 3 S TENSOR REMARK 3 S11: -0.0326 S12: 0.0038 S13: 0.0750 REMARK 3 S21: 0.0447 S22: 0.0085 S23: 0.0310 REMARK 3 S31: -0.0045 S32: -0.1508 S33: 0.0241 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND RESID 608-888 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6162 1.8776 20.6361 REMARK 3 T TENSOR REMARK 3 T11: -0.0239 T22: 0.0013 REMARK 3 T33: 0.0251 T12: 0.0116 REMARK 3 T13: 0.0090 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.9222 L22: 0.5545 REMARK 3 L33: 1.5059 L12: 0.3790 REMARK 3 L13: -0.3239 L23: -0.3065 REMARK 3 S TENSOR REMARK 3 S11: -0.0479 S12: -0.0352 S13: -0.0940 REMARK 3 S21: -0.0443 S22: -0.0100 S23: 0.0140 REMARK 3 S31: 0.0557 S32: -0.1087 S33: 0.0580 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP. REMARK 3 ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY REMARK 4 REMARK 4 2YN8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1290054471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40603 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 89.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7 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 44.76350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 SER A 596 REMARK 465 SER A 597 REMARK 465 ASP A 598 REMARK 465 PRO A 599 REMARK 465 ASN A 600 REMARK 465 GLU A 601 REMARK 465 ALA A 602 REMARK 465 VAL A 603 REMARK 465 ARG A 604 REMARK 465 GLU A 605 REMARK 465 PHE A 606 REMARK 465 ALA A 607 REMARK 465 ALA A 636 REMARK 465 PRO A 637 REMARK 465 GLY A 638 REMARK 465 LYS A 639 REMARK 465 LYS A 640 REMARK 465 GLY A 760 REMARK 465 LEU A 761 REMARK 465 SER A 762 REMARK 465 ARG A 763 REMARK 465 PHE A 764 REMARK 465 LEU A 765 REMARK 465 GLU A 766 REMARK 465 GLU A 767 REMARK 465 ASN A 768 REMARK 465 SER A 769 REMARK 465 SER A 770 REMARK 465 ASP A 771 REMARK 465 PRO A 772 REMARK 465 THR A 773 REMARK 465 GLU A 774 REMARK 465 THR A 775 REMARK 465 SER A 776 REMARK 465 SER A 777 REMARK 465 LEU A 778 REMARK 465 GLY A 779 REMARK 465 GLY A 780 REMARK 465 LYS A 781 REMARK 465 ILE A 782 REMARK 465 ARG A 889 REMARK 465 GLU A 890 REMARK 465 ASN A 891 REMARK 465 GLY A 892 REMARK 465 GLY B 595 REMARK 465 SER B 596 REMARK 465 SER B 597 REMARK 465 ASP B 598 REMARK 465 PRO B 599 REMARK 465 ASN B 600 REMARK 465 GLU B 601 REMARK 465 ALA B 602 REMARK 465 VAL B 603 REMARK 465 ARG B 604 REMARK 465 GLU B 605 REMARK 465 GLY B 760 REMARK 465 LEU B 761 REMARK 465 SER B 762 REMARK 465 ARG B 763 REMARK 465 PHE B 764 REMARK 465 LEU B 765 REMARK 465 GLU B 766 REMARK 465 GLU B 767 REMARK 465 ASN B 768 REMARK 465 SER B 769 REMARK 465 SER B 770 REMARK 465 ASP B 771 REMARK 465 PRO B 772 REMARK 465 THR B 773 REMARK 465 GLU B 774 REMARK 465 THR B 775 REMARK 465 SER B 776 REMARK 465 SER B 777 REMARK 465 LEU B 778 REMARK 465 GLY B 779 REMARK 465 GLY B 780 REMARK 465 LYS B 781 REMARK 465 ILE B 782 REMARK 465 ARG B 889 REMARK 465 GLU B 890 REMARK 465 ASN B 891 REMARK 465 GLY B 892 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 GLU A 625 CG CD OE1 OE2 REMARK 470 LYS A 635 CG CD CE NZ REMARK 470 GLU A 641 CG CD OE1 OE2 REMARK 470 ARG A 656 CG CD NE CZ NH1 NH2 REMARK 470 MET A 687 CG SD CE REMARK 470 ARG A 795 NE CZ NH1 NH2 REMARK 470 LYS A 796 CE NZ REMARK 470 LYS A 859 CD CE NZ REMARK 470 LYS A 885 CD CE NZ REMARK 470 PHE B 606 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 625 CG CD OE1 OE2 REMARK 470 LYS B 635 CG CD CE NZ REMARK 470 LYS B 639 CG CD CE NZ REMARK 470 LYS B 640 CG CD CE NZ REMARK 470 GLU B 733 CD OE1 OE2 REMARK 470 MET B 734 CE REMARK 470 ARG B 795 CD NE CZ NH1 NH2 REMARK 470 LYS B 796 CG CD CE NZ REMARK 470 GLN B 827 CG CD OE1 NE2 REMARK 470 LYS B 876 CD CE NZ REMARK 470 LYS B 885 CG CD CE NZ 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 GLU A 618 -160.34 -119.69 REMARK 500 TYR A 653 147.88 -176.57 REMARK 500 ASN A 708 46.27 -96.83 REMARK 500 ARG A 739 -21.91 71.71 REMARK 500 ASP A 758 85.06 70.32 REMARK 500 TRP A 822 -136.57 50.73 REMARK 500 GLU B 618 -162.18 -111.87 REMARK 500 TYR B 653 146.71 -176.25 REMARK 500 ASN B 708 45.48 -97.63 REMARK 500 ARG B 739 -20.77 76.16 REMARK 500 ASP B 758 85.21 70.17 REMARK 500 TRP B 822 -136.18 51.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2006 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH B2027 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH B2201 DISTANCE = 8.54 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE STU A 1889 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE STU B 1889 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BBA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE AND THERMODYNAMIC CHARACTERIZATION OF THEEPHB4 REMARK 900 RECEPTOR IN COMPLEX WITH AN EPHRIN-B2 ANTAGONISTPEPTIDE REVEALS THE REMARK 900 DETERMINANTS FOR RECEPTOR SPECIFICITY REMARK 900 RELATED ID: 2VWU RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWV RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWW RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWX RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWY RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWZ RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VX0 RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VX1 RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2X9F RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2XVD RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 4AW5 RELATED DB: PDB REMARK 900 COMPLEX OF THE EPHB4 KINASE DOMAIN WITH AN OXINDOLE INHIBITOR REMARK 900 RELATED ID: 4BB4 RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX DBREF 2YN8 A 598 892 UNP P54760 EPHB4_HUMAN 598 892 DBREF 2YN8 B 598 892 UNP P54760 EPHB4_HUMAN 598 892 SEQADV 2YN8 GLY A 595 UNP P54760 EXPRESSION TAG SEQADV 2YN8 SER A 596 UNP P54760 EXPRESSION TAG SEQADV 2YN8 SER A 597 UNP P54760 EXPRESSION TAG SEQADV 2YN8 GLU A 774 UNP P54760 TYR 774 ENGINEERED MUTATION SEQADV 2YN8 VAL A 803 UNP P54760 ALA 803 ENGINEERED MUTATION SEQADV 2YN8 ILE A 870 UNP P54760 VAL 870 ENGINEERED MUTATION SEQADV 2YN8 GLY B 595 UNP P54760 EXPRESSION TAG SEQADV 2YN8 SER B 596 UNP P54760 EXPRESSION TAG SEQADV 2YN8 SER B 597 UNP P54760 EXPRESSION TAG SEQADV 2YN8 GLU B 774 UNP P54760 TYR 774 ENGINEERED MUTATION SEQADV 2YN8 VAL B 803 UNP P54760 ALA 803 ENGINEERED MUTATION SEQADV 2YN8 ILE B 870 UNP P54760 VAL 870 ENGINEERED MUTATION SEQRES 1 A 298 GLY SER SER ASP PRO ASN GLU ALA VAL ARG GLU PHE ALA SEQRES 2 A 298 LYS GLU ILE ASP VAL SER TYR VAL LYS ILE GLU GLU VAL SEQRES 3 A 298 ILE GLY ALA GLY GLU PHE GLY GLU VAL CYS ARG GLY ARG SEQRES 4 A 298 LEU LYS ALA PRO GLY LYS LYS GLU SER CYS VAL ALA ILE SEQRES 5 A 298 LYS THR LEU LYS GLY GLY TYR THR GLU ARG GLN ARG ARG SEQRES 6 A 298 GLU PHE LEU SER GLU ALA SER ILE MET GLY GLN PHE GLU SEQRES 7 A 298 HIS PRO ASN ILE ILE ARG LEU GLU GLY VAL VAL THR ASN SEQRES 8 A 298 SER MET PRO VAL MET ILE LEU THR GLU PHE MET GLU ASN SEQRES 9 A 298 GLY ALA LEU ASP SER PHE LEU ARG LEU ASN ASP GLY GLN SEQRES 10 A 298 PHE THR VAL ILE GLN LEU VAL GLY MET LEU ARG GLY ILE SEQRES 11 A 298 ALA SER GLY MET ARG TYR LEU ALA GLU MET SER TYR VAL SEQRES 12 A 298 HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU VAL ASN SER SEQRES 13 A 298 ASN LEU VAL CYS LYS VAL SER ASP PHE GLY LEU SER ARG SEQRES 14 A 298 PHE LEU GLU GLU ASN SER SER ASP PRO THR GLU THR SER SEQRES 15 A 298 SER LEU GLY GLY LYS ILE PRO ILE ARG TRP THR ALA PRO SEQRES 16 A 298 GLU ALA ILE ALA PHE ARG LYS PHE THR SER ALA SER ASP SEQRES 17 A 298 VAL TRP SER TYR GLY ILE VAL MET TRP GLU VAL MET SER SEQRES 18 A 298 PHE GLY GLU ARG PRO TYR TRP ASP MET SER ASN GLN ASP SEQRES 19 A 298 VAL ILE ASN ALA ILE GLU GLN ASP TYR ARG LEU PRO PRO SEQRES 20 A 298 PRO PRO ASP CYS PRO THR SER LEU HIS GLN LEU MET LEU SEQRES 21 A 298 ASP CYS TRP GLN LYS ASP ARG ASN ALA ARG PRO ARG PHE SEQRES 22 A 298 PRO GLN ILE VAL SER ALA LEU ASP LYS MET ILE ARG ASN SEQRES 23 A 298 PRO ALA SER LEU LYS ILE VAL ALA ARG GLU ASN GLY SEQRES 1 B 298 GLY SER SER ASP PRO ASN GLU ALA VAL ARG GLU PHE ALA SEQRES 2 B 298 LYS GLU ILE ASP VAL SER TYR VAL LYS ILE GLU GLU VAL SEQRES 3 B 298 ILE GLY ALA GLY GLU PHE GLY GLU VAL CYS ARG GLY ARG SEQRES 4 B 298 LEU LYS ALA PRO GLY LYS LYS GLU SER CYS VAL ALA ILE SEQRES 5 B 298 LYS THR LEU LYS GLY GLY TYR THR GLU ARG GLN ARG ARG SEQRES 6 B 298 GLU PHE LEU SER GLU ALA SER ILE MET GLY GLN PHE GLU SEQRES 7 B 298 HIS PRO ASN ILE ILE ARG LEU GLU GLY VAL VAL THR ASN SEQRES 8 B 298 SER MET PRO VAL MET ILE LEU THR GLU PHE MET GLU ASN SEQRES 9 B 298 GLY ALA LEU ASP SER PHE LEU ARG LEU ASN ASP GLY GLN SEQRES 10 B 298 PHE THR VAL ILE GLN LEU VAL GLY MET LEU ARG GLY ILE SEQRES 11 B 298 ALA SER GLY MET ARG TYR LEU ALA GLU MET SER TYR VAL SEQRES 12 B 298 HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU VAL ASN SER SEQRES 13 B 298 ASN LEU VAL CYS LYS VAL SER ASP PHE GLY LEU SER ARG SEQRES 14 B 298 PHE LEU GLU GLU ASN SER SER ASP PRO THR GLU THR SER SEQRES 15 B 298 SER LEU GLY GLY LYS ILE PRO ILE ARG TRP THR ALA PRO SEQRES 16 B 298 GLU ALA ILE ALA PHE ARG LYS PHE THR SER ALA SER ASP SEQRES 17 B 298 VAL TRP SER TYR GLY ILE VAL MET TRP GLU VAL MET SER SEQRES 18 B 298 PHE GLY GLU ARG PRO TYR TRP ASP MET SER ASN GLN ASP SEQRES 19 B 298 VAL ILE ASN ALA ILE GLU GLN ASP TYR ARG LEU PRO PRO SEQRES 20 B 298 PRO PRO ASP CYS PRO THR SER LEU HIS GLN LEU MET LEU SEQRES 21 B 298 ASP CYS TRP GLN LYS ASP ARG ASN ALA ARG PRO ARG PHE SEQRES 22 B 298 PRO GLN ILE VAL SER ALA LEU ASP LYS MET ILE ARG ASN SEQRES 23 B 298 PRO ALA SER LEU LYS ILE VAL ALA ARG GLU ASN GLY HET STU A1889 35 HET STU B1889 35 HETNAM STU STAUROSPORINE FORMUL 3 STU 2(C28 H26 N4 O3) FORMUL 5 HOH *419(H2 O) HELIX 1 1 ASP A 611 SER A 613 5 3 HELIX 2 2 THR A 654 GLN A 670 1 17 HELIX 3 3 LEU A 701 ASN A 708 1 8 HELIX 4 4 THR A 713 MET A 734 1 22 HELIX 5 5 ALA A 742 ARG A 744 5 3 HELIX 6 6 PRO A 783 THR A 787 5 5 HELIX 7 7 ALA A 788 ARG A 795 1 8 HELIX 8 8 THR A 798 SER A 815 1 18 HELIX 9 9 SER A 825 GLN A 835 1 11 HELIX 10 10 PRO A 846 TRP A 857 1 12 HELIX 11 11 ASP A 860 ARG A 864 5 5 HELIX 12 12 ARG A 866 ASN A 880 1 15 HELIX 13 13 PRO A 881 ILE A 886 5 6 HELIX 14 14 ASP B 611 SER B 613 5 3 HELIX 15 15 THR B 654 GLN B 670 1 17 HELIX 16 16 LEU B 701 ASN B 708 1 8 HELIX 17 17 THR B 713 MET B 734 1 22 HELIX 18 18 ALA B 742 ARG B 744 5 3 HELIX 19 19 PRO B 783 THR B 787 5 5 HELIX 20 20 ALA B 788 ARG B 795 1 8 HELIX 21 21 THR B 798 SER B 815 1 18 HELIX 22 22 SER B 825 GLN B 835 1 11 HELIX 23 23 PRO B 846 TRP B 857 1 12 HELIX 24 24 ASP B 860 ARG B 864 5 5 HELIX 25 25 ARG B 866 ASN B 880 1 15 HELIX 26 26 PRO B 881 ILE B 886 5 6 SHEET 1 AA 5 VAL A 615 ALA A 623 0 SHEET 2 AA 5 GLU A 628 LEU A 634 -1 O VAL A 629 N ILE A 621 SHEET 3 AA 5 SER A 642 LEU A 649 -1 O SER A 642 N LEU A 634 SHEET 4 AA 5 VAL A 689 GLU A 694 -1 O VAL A 689 N LEU A 649 SHEET 5 AA 5 LEU A 679 VAL A 683 -1 N GLU A 680 O LEU A 692 SHEET 1 AB 3 GLY A 699 ALA A 700 0 SHEET 2 AB 3 ILE A 746 VAL A 748 -1 N VAL A 748 O GLY A 699 SHEET 3 AB 3 CYS A 754 VAL A 756 -1 O LYS A 755 N LEU A 747 SHEET 1 BA 5 VAL B 615 ALA B 623 0 SHEET 2 BA 5 GLU B 628 LEU B 634 -1 O VAL B 629 N ILE B 621 SHEET 3 BA 5 SER B 642 LEU B 649 -1 O SER B 642 N LEU B 634 SHEET 4 BA 5 VAL B 689 GLU B 694 -1 O VAL B 689 N LEU B 649 SHEET 5 BA 5 LEU B 679 VAL B 683 -1 N GLU B 680 O LEU B 692 SHEET 1 BB 3 GLY B 699 ALA B 700 0 SHEET 2 BB 3 ILE B 746 VAL B 748 -1 N VAL B 748 O GLY B 699 SHEET 3 BB 3 CYS B 754 VAL B 756 -1 O LYS B 755 N LEU B 747 CISPEP 1 MET A 687 PRO A 688 0 3.42 CISPEP 2 MET B 687 PRO B 688 0 1.21 SITE 1 AC1 17 ILE A 621 GLY A 622 ALA A 623 ALA A 645 SITE 2 AC1 17 LYS A 647 GLU A 664 THR A 693 GLU A 694 SITE 3 AC1 17 PHE A 695 MET A 696 GLY A 699 ARG A 744 SITE 4 AC1 17 LEU A 747 SER A 757 ASP A 758 HOH A2127 SITE 5 AC1 17 MET B 687 SITE 1 AC2 15 ILE B 621 GLY B 622 ALA B 623 ALA B 645 SITE 2 AC2 15 LYS B 647 GLU B 664 THR B 693 GLU B 694 SITE 3 AC2 15 PHE B 695 MET B 696 GLY B 699 ARG B 744 SITE 4 AC2 15 LEU B 747 SER B 757 ASP B 758 CRYST1 51.635 89.527 81.087 90.00 103.21 90.00 P 1 21 1 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 0.019367 0.000000 0.004546 0.00000 SCALE2 0.000000 0.011170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012668 0.00000