HEADER TRANSFERASE 12-DEC-12 3ZFY TITLE CRYSTAL STRUCTURE OF EPHB3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 616-910; COMPND 5 SYNONYM: EPH-LIKE TYROSINE KINASE 2, EPH-LIKE KINASE 2, EMBRYONIC COMPND 6 KINASE 2, EK2, HEK2, TYROSINE-PROTEIN KINASE TYRO6, EPHB3; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.DEBRECZENI,R.OVERMAN,C.TRUMAN,M.MCALISTER,T.K.ATTWOOD REVDAT 4 07-MAY-14 3ZFY 1 JRNL REVDAT 3 09-APR-14 3ZFY 1 JRNL REVDAT 2 05-MAR-14 3ZFY 1 JRNL REVDAT 1 08-JAN-14 3ZFY 0 JRNL AUTH R.C.OVERMAN,J.E.DEBRECZENI,C.M.TRUMAN,M.S.MCALISTER, JRNL AUTH 2 T.K.ATTWOOD JRNL TITL COMPLETING THE STRUCTURAL FAMILY PORTRAIT OF THE HUMAN EPHB JRNL TITL 2 TYROSINE KINASE DOMAINS JRNL REF PROTEIN SCI. V. 23 627 2014 JRNL REFN ISSN 0961-8368 JRNL PMID 24677421 JRNL DOI 10.1002/PRO.2445 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 92.30 REMARK 3 NUMBER OF REFLECTIONS : 28046 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) : 0.22552 REMARK 3 R VALUE (WORKING SET) : 0.22406 REMARK 3 FREE R VALUE : 0.25188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1515 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.199 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.256 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1679 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.286 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.316 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3989 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.017 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.78 REMARK 3 B22 (A**2) : -1.99 REMARK 3 B33 (A**2) : 4.75 REMARK 3 B12 (A**2) : 0.18 REMARK 3 B13 (A**2) : 0.09 REMARK 3 B23 (A**2) : -0.18 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.307 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.171 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4070 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2701 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5532 ; 1.274 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6571 ; 0.934 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 5.894 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;34.623 ;23.736 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 658 ;14.353 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.167 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4500 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 832 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 595 A 892 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1726 -1.5420 -0.1587 REMARK 3 T TENSOR REMARK 3 T11: 0.1430 T22: 0.1461 REMARK 3 T33: 0.0584 T12: 0.0273 REMARK 3 T13: -0.0079 T23: -0.0369 REMARK 3 L TENSOR REMARK 3 L11: 3.0230 L22: 3.6200 REMARK 3 L33: 1.0506 L12: -0.2783 REMARK 3 L13: -0.0594 L23: -0.0189 REMARK 3 S TENSOR REMARK 3 S11: -0.0834 S12: -0.6024 S13: 0.2217 REMARK 3 S21: 0.6995 S22: 0.1168 S23: -0.0178 REMARK 3 S31: -0.0826 S32: 0.0722 S33: -0.0334 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 595 B 892 REMARK 3 ORIGIN FOR THE GROUP (A): 31.7141 -29.9917 -23.2166 REMARK 3 T TENSOR REMARK 3 T11: 0.1368 T22: 0.1598 REMARK 3 T33: 0.0319 T12: -0.0299 REMARK 3 T13: -0.0067 T23: 0.0633 REMARK 3 L TENSOR REMARK 3 L11: 3.7413 L22: 3.9565 REMARK 3 L33: 1.2514 L12: 0.4588 REMARK 3 L13: 0.0061 L23: 0.4793 REMARK 3 S TENSOR REMARK 3 S11: -0.1463 S12: 0.7243 S13: 0.2697 REMARK 3 S21: -0.7211 S22: 0.1430 S23: 0.0275 REMARK 3 S31: -0.1512 S32: -0.0920 S33: 0.0033 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 3ZFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-DEC-12. REMARK 100 THE PDBE ID CODE IS EBI-55106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29560 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 61.20 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 2.0 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.68 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.9 REMARK 200 R MERGE FOR SHELL (I) : 0.14 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.83 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 613 REMARK 465 SER A 614 REMARK 465 SER A 615 REMARK 465 ASP A 616 REMARK 465 PRO A 617 REMARK 465 ASN A 618 REMARK 465 GLU A 619 REMARK 465 ALA A 620 REMARK 465 VAL A 621 REMARK 465 ARG A 622 REMARK 465 GLU A 623 REMARK 465 PHE A 624 REMARK 465 ALA A 625 REMARK 465 LYS A 626 REMARK 465 GLU A 627 REMARK 465 ILE A 628 REMARK 465 ASP A 629 REMARK 465 VAL A 630 REMARK 465 SER A 631 REMARK 465 ILE A 639 REMARK 465 GLY A 640 REMARK 465 ALA A 641 REMARK 465 GLY A 642 REMARK 465 GLY A 656 REMARK 465 ARG A 657 REMARK 465 LEU A 779 REMARK 465 SER A 780 REMARK 465 ARG A 781 REMARK 465 PHE A 782 REMARK 465 LEU A 783 REMARK 465 LEU A 796 REMARK 465 GLY A 797 REMARK 465 GLY A 798 REMARK 465 ALA A 906 REMARK 465 SER A 907 REMARK 465 ALA A 908 REMARK 465 GLN A 909 REMARK 465 SER A 910 REMARK 465 GLY B 613 REMARK 465 SER B 614 REMARK 465 SER B 615 REMARK 465 ASP B 616 REMARK 465 PRO B 617 REMARK 465 ASN B 618 REMARK 465 GLU B 619 REMARK 465 ALA B 620 REMARK 465 VAL B 621 REMARK 465 ARG B 622 REMARK 465 GLU B 623 REMARK 465 PHE B 624 REMARK 465 ALA B 625 REMARK 465 LYS B 626 REMARK 465 GLU B 627 REMARK 465 ILE B 628 REMARK 465 ASP B 629 REMARK 465 VAL B 630 REMARK 465 ILE B 639 REMARK 465 GLY B 640 REMARK 465 ALA B 641 REMARK 465 GLY B 642 REMARK 465 GLU B 643 REMARK 465 PRO B 655 REMARK 465 GLY B 656 REMARK 465 LYS B 668 REMARK 465 VAL B 669 REMARK 465 GLY B 670 REMARK 465 TYR B 671 REMARK 465 THR B 672 REMARK 465 LEU B 779 REMARK 465 SER B 780 REMARK 465 ARG B 781 REMARK 465 PHE B 782 REMARK 465 LEU B 783 REMARK 465 LEU B 796 REMARK 465 GLY B 797 REMARK 465 GLY B 798 REMARK 465 ALA B 906 REMARK 465 SER B 907 REMARK 465 ALA B 908 REMARK 465 GLN B 909 REMARK 465 SER B 910 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 LYS A 634 CG CD CE NZ REMARK 470 GLU A 636 CG CD OE1 OE2 REMARK 470 GLU A 637 CG CD OE1 OE2 REMARK 470 GLU A 646 CG CD OE1 OE2 REMARK 470 ARG A 649 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 651 CZ NH1 NH2 REMARK 470 LYS A 653 CG CD CE NZ REMARK 470 GLN A 654 CG CD OE1 NE2 REMARK 470 ARG A 658 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 668 CG CD CE NZ REMARK 470 VAL A 669 CG1 CG2 REMARK 470 THR A 672 OG1 CG2 REMARK 470 GLU A 673 CG CD OE1 OE2 REMARK 470 ARG A 674 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 675 CG CD OE1 NE2 REMARK 470 ARG A 677 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 688 CD OE1 NE2 REMARK 470 LYS A 703 CG CD CE NZ REMARK 470 ARG A 705 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 799 CG CD CE NZ REMARK 470 ARG A 813 NE CZ NH1 NH2 REMARK 470 LYS B 634 CG CD CE NZ REMARK 470 GLU B 636 CG CD OE1 OE2 REMARK 470 GLU B 637 CG CD OE1 OE2 REMARK 470 GLU B 646 CG CD OE1 OE2 REMARK 470 ARG B 649 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 651 CZ NH1 NH2 REMARK 470 LYS B 653 CG CD CE NZ REMARK 470 GLN B 654 CG CD OE1 NE2 REMARK 470 ARG B 657 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 658 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 665 CG CD CE NZ REMARK 470 GLU B 673 CG CD OE1 OE2 REMARK 470 ARG B 674 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 675 CG CD OE1 NE2 REMARK 470 ARG B 677 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 688 CD OE1 NE2 REMARK 470 LYS B 703 CG CD CE NZ REMARK 470 ARG B 705 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 799 CG CD CE NZ REMARK 470 ARG B 813 NE CZ NH1 NH2 REMARK 470 LYS B 884 CE NZ REMARK 470 LYS B 903 CE NZ 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 ARG A 696 NE - CZ - NH1 ANGL. DEV. = 3.2 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 GLU A 636 -150.73 -106.76 REMARK 500 GLU A 637 107.88 -29.53 REMARK 500 ASP A 690 104.34 -160.16 REMARK 500 CYS A 717 -149.02 57.73 REMARK 500 ARG A 757 -17.57 81.22 REMARK 500 ASP A 758 44.75 -141.84 REMARK 500 ASP A 789 65.82 -119.25 REMARK 500 TRP A 840 -125.91 43.52 REMARK 500 CYS B 632 -0.70 -58.45 REMARK 500 GLU B 636 -151.07 -105.32 REMARK 500 GLU B 637 107.37 -29.04 REMARK 500 ASP B 690 104.69 -161.23 REMARK 500 CYS B 717 -148.97 57.43 REMARK 500 ARG B 757 -17.00 82.24 REMARK 500 ASP B 758 44.30 -143.92 REMARK 500 PHE B 777 29.53 44.96 REMARK 500 ASP B 789 67.34 -118.65 REMARK 500 TRP B 840 -126.14 44.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZEW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF EPHB4 IN COMPLEX WITH STAUROSPORINE REMARK 900 RELATED ID: 3ZFM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF EPHB2 REMARK 900 RELATED ID: 3ZFX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF EPHB1 DBREF 3ZFY A 616 910 UNP P54753 EPHB3_HUMAN 616 910 DBREF 3ZFY B 616 910 UNP P54753 EPHB3_HUMAN 616 910 SEQADV 3ZFY GLY A 613 UNP P54753 EXPRESSION TAG SEQADV 3ZFY SER A 614 UNP P54753 EXPRESSION TAG SEQADV 3ZFY SER A 615 UNP P54753 EXPRESSION TAG SEQADV 3ZFY PRO A 899 UNP P54753 ALA 899 CONFLICT SEQADV 3ZFY GLY B 613 UNP P54753 EXPRESSION TAG SEQADV 3ZFY SER B 614 UNP P54753 EXPRESSION TAG SEQADV 3ZFY SER B 615 UNP P54753 EXPRESSION TAG SEQADV 3ZFY PRO B 899 UNP P54753 ALA 899 CONFLICT 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 CYS 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 GLN PRO GLY ARG ARG GLU VAL PHE VAL ALA ILE SEQRES 5 A 298 LYS THR LEU LYS VAL GLY TYR THR GLU ARG GLN ARG ARG SEQRES 6 A 298 ASP PHE LEU SER GLU ALA SER ILE MET GLY GLN PHE ASP SEQRES 7 A 298 HIS PRO ASN ILE ILE ARG LEU GLU GLY VAL VAL THR LYS SEQRES 8 A 298 SER ARG PRO VAL MET ILE LEU THR GLU PHE MET GLU ASN SEQRES 9 A 298 CYS 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 ALA GLY MET LYS TYR LEU SER GLU MET ASN 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 ASP ASP PRO SER ASP PRO THR TYR 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 TYR 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 TYR GLY GLU ARG PRO TYR TRP ASP MET SER ASN GLN ASP SEQRES 19 A 298 VAL ILE ASN ALA VAL GLU GLN ASP TYR ARG LEU PRO PRO SEQRES 20 A 298 PRO MET ASP CYS PRO THR ALA LEU HIS GLN LEU MET LEU SEQRES 21 A 298 ASP CYS TRP VAL ARG ASP ARG ASN LEU ARG PRO LYS PHE SEQRES 22 A 298 SER GLN ILE VAL ASN THR LEU ASP LYS LEU ILE ARG ASN SEQRES 23 A 298 PRO ALA SER LEU LYS VAL ILE ALA SER ALA GLN SER 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 CYS 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 GLN PRO GLY ARG ARG GLU VAL PHE VAL ALA ILE SEQRES 5 B 298 LYS THR LEU LYS VAL GLY TYR THR GLU ARG GLN ARG ARG SEQRES 6 B 298 ASP PHE LEU SER GLU ALA SER ILE MET GLY GLN PHE ASP SEQRES 7 B 298 HIS PRO ASN ILE ILE ARG LEU GLU GLY VAL VAL THR LYS SEQRES 8 B 298 SER ARG PRO VAL MET ILE LEU THR GLU PHE MET GLU ASN SEQRES 9 B 298 CYS 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 ALA GLY MET LYS TYR LEU SER GLU MET ASN 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 ASP ASP PRO SER ASP PRO THR TYR 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 TYR 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 TYR GLY GLU ARG PRO TYR TRP ASP MET SER ASN GLN ASP SEQRES 19 B 298 VAL ILE ASN ALA VAL GLU GLN ASP TYR ARG LEU PRO PRO SEQRES 20 B 298 PRO MET ASP CYS PRO THR ALA LEU HIS GLN LEU MET LEU SEQRES 21 B 298 ASP CYS TRP VAL ARG ASP ARG ASN LEU ARG PRO LYS PHE SEQRES 22 B 298 SER GLN ILE VAL ASN THR LEU ASP LYS LEU ILE ARG ASN SEQRES 23 B 298 PRO ALA SER LEU LYS VAL ILE ALA SER ALA GLN SER FORMUL 2 HOH *128(H2 O) HELIX 1 1 THR A 672 GLY A 687 1 16 HELIX 2 2 ALA A 718 ASN A 726 1 9 HELIX 3 3 THR A 731 MET A 752 1 22 HELIX 4 4 ALA A 760 ARG A 762 5 3 HELIX 5 5 PRO A 801 THR A 805 5 5 HELIX 6 6 ALA A 806 ARG A 813 1 8 HELIX 7 7 THR A 816 SER A 833 1 18 HELIX 8 8 SER A 843 GLN A 853 1 11 HELIX 9 9 PRO A 864 TRP A 875 1 12 HELIX 10 10 ASP A 878 ARG A 882 5 5 HELIX 11 11 LYS A 884 ASN A 898 1 15 HELIX 12 12 PRO A 899 VAL A 904 5 6 HELIX 13 13 GLU B 673 GLY B 687 1 15 HELIX 14 14 ALA B 718 ASN B 726 1 9 HELIX 15 15 THR B 731 MET B 752 1 22 HELIX 16 16 ALA B 760 ARG B 762 5 3 HELIX 17 17 PRO B 801 THR B 805 5 5 HELIX 18 18 ALA B 806 ARG B 813 1 8 HELIX 19 19 THR B 816 SER B 833 1 18 HELIX 20 20 SER B 843 GLN B 853 1 11 HELIX 21 21 PRO B 864 TRP B 875 1 12 HELIX 22 22 ASP B 878 ARG B 882 5 5 HELIX 23 23 LYS B 884 ASN B 898 1 15 HELIX 24 24 PRO B 899 VAL B 904 5 6 SHEET 1 AA 5 VAL A 633 ILE A 635 0 SHEET 2 AA 5 CYS A 648 LEU A 652 -1 O ARG A 651 N LYS A 634 SHEET 3 AA 5 VAL A 660 LYS A 665 -1 O VAL A 660 N LEU A 652 SHEET 4 AA 5 MET A 708 GLU A 712 -1 O ILE A 709 N LYS A 665 SHEET 5 AA 5 LEU A 697 VAL A 701 -1 O GLY A 699 N LEU A 710 SHEET 1 AB 2 ILE A 764 VAL A 766 0 SHEET 2 AB 2 CYS A 772 VAL A 774 -1 O LYS A 773 N LEU A 765 SHEET 1 BA 5 VAL B 633 ILE B 635 0 SHEET 2 BA 5 CYS B 648 LEU B 652 -1 O ARG B 651 N LYS B 634 SHEET 3 BA 5 VAL B 660 LYS B 665 -1 O VAL B 660 N LEU B 652 SHEET 4 BA 5 MET B 708 GLU B 712 -1 O ILE B 709 N LYS B 665 SHEET 5 BA 5 LEU B 697 VAL B 701 -1 O GLY B 699 N LEU B 710 SHEET 1 BB 2 ILE B 764 VAL B 766 0 SHEET 2 BB 2 CYS B 772 VAL B 774 -1 O LYS B 773 N LEU B 765 CISPEP 1 ARG A 705 PRO A 706 0 5.68 CISPEP 2 ARG B 705 PRO B 706 0 5.32 CRYST1 46.990 56.488 61.354 93.02 90.65 90.03 P 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 0.021281 0.000011 0.000242 0.00000 SCALE2 0.000000 0.017703 0.000934 0.00000 SCALE3 0.000000 0.000000 0.016323 0.00000