PDB Short entry for 5MJB HEADER TRANSFERASE 30-NOV-16 5MJB TITLE KINASE DOMAIN OF HUMAN EPHB1, G703C MUTANT, COVALENTLY BOUND TO A TITLE 2 QUINAZOLINE-BASED INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ELK,EPH TYROSINE KINASE 2,EPH-LIKE KINASE 6,HEK6,NEURONALLY- COMPND 5 EXPRESSED EPH-RELATED TYROSINE KINASE,NET,TYROSINE-PROTEIN KINASE COMPND 6 RECEPTOR EPH-2; 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 GENE: EPHB1, ELK, EPHT2, HEK6, NET; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD KEYWDS RECEPTOR TYROSINE KINASE, KINASE DOMAIN, INHIBITOR, COVALENT, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUNG,M.SCHIMPL,Y.-C.CHEN,R.C.OVERMAN,C.ZHANG REVDAT 3 17-JAN-24 5MJB 1 REMARK REVDAT 2 28-JUN-17 5MJB 1 JRNL REVDAT 1 17-MAY-17 5MJB 0 JRNL AUTH A.KUNG,M.SCHIMPL,A.EKANAYAKE,Y.C.CHEN,R.OVERMAN,C.ZHANG JRNL TITL A CHEMICAL-GENETIC APPROACH TO GENERATE SELECTIVE COVALENT JRNL TITL 2 INHIBITORS OF PROTEIN KINASES. JRNL REF ACS CHEM. BIOL. V. 12 1499 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28459525 JRNL DOI 10.1021/ACSCHEMBIO.6B01083 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.6 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 46452 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2232 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 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) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.29 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.43 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3372 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3090 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3201 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 171 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4418 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84470 REMARK 3 B22 (A**2) : 0.84470 REMARK 3 B33 (A**2) : -1.68950 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.300 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.186 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.153 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.182 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.152 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 : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4582 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6205 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1586 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 104 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 659 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4582 ; 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 : 577 ; 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 : 5267 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.23 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.08 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -1.8574 39.7546 -3.0785 REMARK 3 T TENSOR REMARK 3 T11: -0.2222 T22: -0.1463 REMARK 3 T33: -0.0630 T12: 0.0709 REMARK 3 T13: -0.0060 T23: -0.0412 REMARK 3 L TENSOR REMARK 3 L11: 2.3198 L22: 2.0110 REMARK 3 L33: 2.4874 L12: 0.1133 REMARK 3 L13: 0.2108 L23: -0.3148 REMARK 3 S TENSOR REMARK 3 S11: -0.2232 S12: -0.1773 S13: -0.0934 REMARK 3 S21: 0.1916 S22: 0.2175 S23: -0.4674 REMARK 3 S31: 0.0802 S32: 0.0216 S33: 0.0057 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -33.2387 40.0775 -6.3115 REMARK 3 T TENSOR REMARK 3 T11: -0.2367 T22: 0.0223 REMARK 3 T33: -0.1116 T12: 0.0583 REMARK 3 T13: 0.0539 T23: 0.1208 REMARK 3 L TENSOR REMARK 3 L11: 2.5028 L22: 1.3281 REMARK 3 L33: 1.4634 L12: 0.3545 REMARK 3 L13: 0.8047 L23: 0.1596 REMARK 3 S TENSOR REMARK 3 S11: -0.1315 S12: -0.1765 S13: 0.0926 REMARK 3 S21: 0.1198 S22: 0.2113 S23: 0.2605 REMARK 3 S31: -0.0888 S32: -0.1992 S33: -0.0798 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-16 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47109 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 58.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 1.70700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: 3ZFX REMARK 200 REMARK 200 REMARK: HEXAGONAL PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18 % PEG3350, 0.1-0.2 M AMMONIUM REMARK 280 SULFATE AND 0.1 M PCTP (SODIUM PROPIONATE, SODIUM CACODYLATE REMARK 280 TRIHYDRATE, BIS-TRIS PROPANE) BUFFER PH 6-9, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.51667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.03333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 105.03333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.51667 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1058 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1092 LIES ON A SPECIAL POSITION. 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 MET A 592 REMARK 465 GLY A 593 REMARK 465 HIS A 594 REMARK 465 HIS A 595 REMARK 465 HIS A 596 REMARK 465 HIS A 597 REMARK 465 HIS A 598 REMARK 465 HIS A 599 REMARK 465 GLY A 600 REMARK 465 SER A 601 REMARK 465 ASP A 602 REMARK 465 PRO A 603 REMARK 465 ASN A 604 REMARK 465 GLU A 605 REMARK 465 ALA A 606 REMARK 465 VAL A 607 REMARK 465 GLN A 770 REMARK 465 ASP A 771 REMARK 465 ASP A 772 REMARK 465 THR A 773 REMARK 465 SER A 774 REMARK 465 ASP A 775 REMARK 465 ALA A 892 REMARK 465 THR A 893 REMARK 465 ILE A 894 REMARK 465 THR A 895 REMARK 465 ALA A 896 REMARK 465 MET B 592 REMARK 465 GLY B 593 REMARK 465 HIS B 594 REMARK 465 HIS B 595 REMARK 465 HIS B 596 REMARK 465 HIS B 597 REMARK 465 HIS B 598 REMARK 465 HIS B 599 REMARK 465 GLY B 600 REMARK 465 SER B 601 REMARK 465 ASP B 602 REMARK 465 PRO B 603 REMARK 465 ASN B 604 REMARK 465 GLU B 605 REMARK 465 ALA B 606 REMARK 465 VAL B 607 REMARK 465 GLN B 770 REMARK 465 ASP B 771 REMARK 465 ASP B 772 REMARK 465 VAL B 891 REMARK 465 ALA B 892 REMARK 465 THR B 893 REMARK 465 ILE B 894 REMARK 465 THR B 895 REMARK 465 ALA B 896 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 ARG A 608 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 620 CD CE NZ REMARK 470 ILE A 786 CG1 CG2 CD1 REMARK 470 LYS A 889 CE NZ REMARK 470 THR A 890 OG1 CG2 REMARK 470 VAL A 891 CG1 CG2 REMARK 470 ARG B 608 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 609 CG CD OE1 OE2 REMARK 470 LYS B 620 CD CE NZ REMARK 470 GLU B 629 CG CD OE1 OE2 REMARK 470 GLU B 632 CG CD OE1 OE2 REMARK 470 LYS B 654 CG CD CE NZ REMARK 470 GLU B 659 CG CD OE1 OE2 REMARK 470 LYS B 660 CD CE NZ REMARK 470 ARG B 663 NE CZ NH1 NH2 REMARK 470 ARG B 678 NE CZ NH1 NH2 REMARK 470 ARG B 691 CG CD NE CZ NH1 NH2 REMARK 470 THR B 773 OG1 CG2 REMARK 470 SER B 774 OG REMARK 470 GLU B 838 CD OE1 OE2 REMARK 470 LYS B 889 CG CD CE NZ REMARK 470 THR B 890 OG1 CG2 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 622 -135.61 -118.57 REMARK 500 CYS A 703 -149.29 56.04 REMARK 500 ASN A 739 33.63 70.17 REMARK 500 ARG A 743 -5.93 70.23 REMARK 500 ASP A 762 70.74 59.63 REMARK 500 TRP A 826 -118.26 50.26 REMARK 500 GLU B 622 -140.95 -119.09 REMARK 500 ARG B 691 -72.75 -47.83 REMARK 500 CYS B 703 -149.49 56.58 REMARK 500 ASN B 739 33.85 70.32 REMARK 500 ARG B 743 -5.40 72.88 REMARK 500 ASP B 762 72.11 57.06 REMARK 500 SER B 774 -89.14 64.85 REMARK 500 TRP B 826 -122.76 52.16 REMARK 500 LYS B 889 -84.54 -62.29 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 7O3 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 7O3 B 901 and CYS B REMARK 800 703 DBREF 5MJB A 602 896 UNP P54762 EPHB1_HUMAN 602 896 DBREF 5MJB B 602 896 UNP P54762 EPHB1_HUMAN 602 896 SEQADV 5MJB MET A 592 UNP P54762 INITIATING METHIONINE SEQADV 5MJB GLY A 593 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS A 594 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS A 595 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS A 596 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS A 597 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS A 598 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS A 599 UNP P54762 EXPRESSION TAG SEQADV 5MJB GLY A 600 UNP P54762 EXPRESSION TAG SEQADV 5MJB SER A 601 UNP P54762 EXPRESSION TAG SEQADV 5MJB ARG A 678 UNP P54762 PRO 678 CONFLICT SEQADV 5MJB CYS A 703 UNP P54762 GLY 703 CONFLICT SEQADV 5MJB SER A 736 UNP P54762 ALA 736 CONFLICT SEQADV 5MJB MET B 592 UNP P54762 INITIATING METHIONINE SEQADV 5MJB GLY B 593 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS B 594 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS B 595 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS B 596 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS B 597 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS B 598 UNP P54762 EXPRESSION TAG SEQADV 5MJB HIS B 599 UNP P54762 EXPRESSION TAG SEQADV 5MJB GLY B 600 UNP P54762 EXPRESSION TAG SEQADV 5MJB SER B 601 UNP P54762 EXPRESSION TAG SEQADV 5MJB ARG B 678 UNP P54762 PRO 678 CONFLICT SEQADV 5MJB CYS B 703 UNP P54762 GLY 703 CONFLICT SEQADV 5MJB SER B 736 UNP P54762 ALA 736 CONFLICT SEQRES 1 A 305 MET GLY HIS HIS HIS HIS HIS HIS GLY SER ASP PRO ASN SEQRES 2 A 305 GLU ALA VAL ARG GLU PHE ALA LYS GLU ILE ASP VAL SER SEQRES 3 A 305 PHE VAL LYS ILE GLU GLU VAL ILE GLY ALA GLY GLU PHE SEQRES 4 A 305 GLY GLU VAL TYR LYS GLY ARG LEU LYS LEU PRO GLY LYS SEQRES 5 A 305 ARG GLU ILE PTR VAL ALA ILE LYS THR LEU LYS ALA GLY SEQRES 6 A 305 TYR SER GLU LYS GLN ARG ARG ASP PHE LEU SER GLU ALA SEQRES 7 A 305 SER ILE MET GLY GLN PHE ASP HIS ARG ASN ILE ILE ARG SEQRES 8 A 305 LEU GLU GLY VAL VAL THR LYS SER ARG PRO VAL MET ILE SEQRES 9 A 305 ILE THR GLU PHE MET GLU ASN CYS ALA LEU ASP SER PHE SEQRES 10 A 305 LEU ARG GLN ASN ASP GLY GLN PHE THR VAL ILE GLN LEU SEQRES 11 A 305 VAL GLY MET LEU ARG GLY ILE ALA ALA GLY MET LYS TYR SEQRES 12 A 305 LEU SER GLU MET ASN TYR VAL HIS ARG ASP LEU ALA ALA SEQRES 13 A 305 ARG ASN ILE LEU VAL ASN SER ASN LEU VAL CYS LYS VAL SEQRES 14 A 305 SER ASP PHE GLY LEU SER ARG TYR LEU GLN ASP ASP THR SEQRES 15 A 305 SER ASP PRO THR PTR THR SER SER LEU GLY GLY LYS ILE SEQRES 16 A 305 PRO VAL ARG TRP THR ALA PRO GLU ALA ILE ALA TYR ARG SEQRES 17 A 305 LYS PHE THR SER ALA SER ASP VAL TRP SER TYR GLY ILE SEQRES 18 A 305 VAL MET TRP GLU VAL MET SER PHE GLY GLU ARG PRO TYR SEQRES 19 A 305 TRP ASP MET SER ASN GLN ASP VAL ILE ASN ALA ILE GLU SEQRES 20 A 305 GLN ASP TYR ARG LEU PRO PRO PRO MET ASP CYS PRO ALA SEQRES 21 A 305 ALA LEU HIS GLN LEU MET LEU ASP CYS TRP GLN LYS ASP SEQRES 22 A 305 ARG ASN SER ARG PRO ARG PHE ALA GLU ILE VAL ASN THR SEQRES 23 A 305 LEU ASP LYS MET ILE ARG ASN PRO ALA SER LEU LYS THR SEQRES 24 A 305 VAL ALA THR ILE THR ALA SEQRES 1 B 305 MET GLY HIS HIS HIS HIS HIS HIS GLY SER ASP PRO ASN SEQRES 2 B 305 GLU ALA VAL ARG GLU PHE ALA LYS GLU ILE ASP VAL SER SEQRES 3 B 305 PHE VAL LYS ILE GLU GLU VAL ILE GLY ALA GLY GLU PHE SEQRES 4 B 305 GLY GLU VAL TYR LYS GLY ARG LEU LYS LEU PRO GLY LYS SEQRES 5 B 305 ARG GLU ILE PTR VAL ALA ILE LYS THR LEU LYS ALA GLY SEQRES 6 B 305 TYR SER GLU LYS GLN ARG ARG ASP PHE LEU SER GLU ALA SEQRES 7 B 305 SER ILE MET GLY GLN PHE ASP HIS ARG ASN ILE ILE ARG SEQRES 8 B 305 LEU GLU GLY VAL VAL THR LYS SER ARG PRO VAL MET ILE SEQRES 9 B 305 ILE THR GLU PHE MET GLU ASN CYS ALA LEU ASP SER PHE SEQRES 10 B 305 LEU ARG GLN ASN ASP GLY GLN PHE THR VAL ILE GLN LEU SEQRES 11 B 305 VAL GLY MET LEU ARG GLY ILE ALA ALA GLY MET LYS TYR SEQRES 12 B 305 LEU SER GLU MET ASN TYR VAL HIS ARG ASP LEU ALA ALA SEQRES 13 B 305 ARG ASN ILE LEU VAL ASN SER ASN LEU VAL CYS LYS VAL SEQRES 14 B 305 SER ASP PHE GLY LEU SER ARG TYR LEU GLN ASP ASP THR SEQRES 15 B 305 SER ASP PRO THR PTR THR SER SER LEU GLY GLY LYS ILE SEQRES 16 B 305 PRO VAL ARG TRP THR ALA PRO GLU ALA ILE ALA TYR ARG SEQRES 17 B 305 LYS PHE THR SER ALA SER ASP VAL TRP SER TYR GLY ILE SEQRES 18 B 305 VAL MET TRP GLU VAL MET SER PHE GLY GLU ARG PRO TYR SEQRES 19 B 305 TRP ASP MET SER ASN GLN ASP VAL ILE ASN ALA ILE GLU SEQRES 20 B 305 GLN ASP TYR ARG LEU PRO PRO PRO MET ASP CYS PRO ALA SEQRES 21 B 305 ALA LEU HIS GLN LEU MET LEU ASP CYS TRP GLN LYS ASP SEQRES 22 B 305 ARG ASN SER ARG PRO ARG PHE ALA GLU ILE VAL ASN THR SEQRES 23 B 305 LEU ASP LYS MET ILE ARG ASN PRO ALA SER LEU LYS THR SEQRES 24 B 305 VAL ALA THR ILE THR ALA MODRES 5MJB PTR A 647 TYR MODIFIED RESIDUE MODRES 5MJB PTR A 778 TYR MODIFIED RESIDUE MODRES 5MJB PTR B 647 TYR MODIFIED RESIDUE MODRES 5MJB PTR B 778 TYR MODIFIED RESIDUE HET PTR A 647 16 HET PTR A 778 16 HET PTR B 647 16 HET PTR B 778 16 HET 7O3 A 901 23 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET 7O3 B 901 23 HET SO4 B 902 5 HET SO4 B 903 5 HETNAM PTR O-PHOSPHOTYROSINE HETNAM 7O3 2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL) HETNAM 2 7O3 AMINO]QUINAZOLIN-7-YL]ETHANAMIDE HETNAM SO4 SULFATE ION HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR 4(C9 H12 N O6 P) FORMUL 3 7O3 2(C16 H12 CL2 N4 O2) FORMUL 4 SO4 5(O4 S 2-) FORMUL 10 HOH *220(H2 O) HELIX 1 AA1 ASP A 615 SER A 617 5 3 HELIX 2 AA2 SER A 658 GLY A 673 1 16 HELIX 3 AA3 ALA A 704 GLN A 711 1 8 HELIX 4 AA4 THR A 717 MET A 738 1 22 HELIX 5 AA5 ALA A 746 ARG A 748 5 3 HELIX 6 AA6 PRO A 787 THR A 791 5 5 HELIX 7 AA7 ALA A 792 ARG A 799 1 8 HELIX 8 AA8 THR A 802 SER A 819 1 18 HELIX 9 AA9 SER A 829 GLN A 839 1 11 HELIX 10 AB1 PRO A 850 TRP A 861 1 12 HELIX 11 AB2 ASP A 864 ARG A 868 5 5 HELIX 12 AB3 ARG A 870 ASN A 884 1 15 HELIX 13 AB4 PRO A 885 LYS A 889 5 5 HELIX 14 AB5 ASP B 615 SER B 617 5 3 HELIX 15 AB6 SER B 658 GLY B 673 1 16 HELIX 16 AB7 ALA B 704 GLN B 711 1 8 HELIX 17 AB8 THR B 717 MET B 738 1 22 HELIX 18 AB9 ALA B 746 ARG B 748 5 3 HELIX 19 AC1 PRO B 787 THR B 791 5 5 HELIX 20 AC2 ALA B 792 ARG B 799 1 8 HELIX 21 AC3 THR B 802 SER B 819 1 18 HELIX 22 AC4 SER B 829 GLN B 839 1 11 HELIX 23 AC5 PRO B 850 TRP B 861 1 12 HELIX 24 AC6 ASP B 864 ARG B 868 5 5 HELIX 25 AC7 ARG B 870 ASN B 884 1 15 HELIX 26 AC8 PRO B 885 LYS B 889 5 5 SHEET 1 AA1 5 VAL A 619 ALA A 627 0 SHEET 2 AA1 5 GLU A 632 LEU A 638 -1 O LYS A 635 N GLU A 623 SHEET 3 AA1 5 ILE A 646 THR A 652 -1 O ILE A 650 N TYR A 634 SHEET 4 AA1 5 MET A 694 GLU A 698 -1 O ILE A 695 N LYS A 651 SHEET 5 AA1 5 LEU A 683 VAL A 687 -1 N GLY A 685 O ILE A 696 SHEET 1 AA2 2 TYR A 740 VAL A 741 0 SHEET 2 AA2 2 ARG A 767 TYR A 768 -1 O ARG A 767 N VAL A 741 SHEET 1 AA3 2 ILE A 750 VAL A 752 0 SHEET 2 AA3 2 CYS A 758 VAL A 760 -1 O LYS A 759 N LEU A 751 SHEET 1 AA4 2 PTR A 778 THR A 779 0 SHEET 2 AA4 2 LYS A 800 PHE A 801 -1 O PHE A 801 N PTR A 778 SHEET 1 AA5 5 VAL B 619 ALA B 627 0 SHEET 2 AA5 5 GLU B 632 LEU B 638 -1 O LYS B 635 N GLU B 623 SHEET 3 AA5 5 ILE B 646 THR B 652 -1 O ILE B 650 N TYR B 634 SHEET 4 AA5 5 MET B 694 GLU B 698 -1 O ILE B 695 N LYS B 651 SHEET 5 AA5 5 LEU B 683 VAL B 687 -1 N GLY B 685 O ILE B 696 SHEET 1 AA6 2 TYR B 740 VAL B 741 0 SHEET 2 AA6 2 ARG B 767 TYR B 768 -1 O ARG B 767 N VAL B 741 SHEET 1 AA7 2 ILE B 750 VAL B 752 0 SHEET 2 AA7 2 CYS B 758 VAL B 760 -1 O LYS B 759 N LEU B 751 SHEET 1 AA8 2 PTR B 778 THR B 779 0 SHEET 2 AA8 2 LYS B 800 PHE B 801 -1 O PHE B 801 N PTR B 778 LINK C ILE A 646 N PTR A 647 1555 1555 1.33 LINK C PTR A 647 N VAL A 648 1555 1555 1.32 LINK SG CYS A 703 C7 7O3 A 901 1555 1555 1.82 LINK C THR A 777 N PTR A 778 1555 1555 1.34 LINK C PTR A 778 N THR A 779 1555 1555 1.34 LINK C ILE B 646 N PTR B 647 1555 1555 1.33 LINK C PTR B 647 N VAL B 648 1555 1555 1.33 LINK SG CYS B 703 C7 7O3 B 901 1555 1555 1.82 LINK C THR B 777 N PTR B 778 1555 1555 1.33 LINK C PTR B 778 N THR B 779 1555 1555 1.33 CISPEP 1 ARG A 691 PRO A 692 0 0.78 SITE 1 AC1 13 ALA A 649 LYS A 651 GLU A 668 THR A 697 SITE 2 AC1 13 GLU A 698 PHE A 699 MET A 700 CYS A 703 SITE 3 AC1 13 LEU A 751 SER A 761 ASP A 762 HOH A1047 SITE 4 AC1 13 HOH A1088 SITE 1 AC2 6 ARG A 678 ARG A 682 LYS A 759 HOH A1013 SITE 2 AC2 6 HOH A1045 HOH A1076 SITE 1 AC3 3 SER A 707 ARG A 710 GLN A 711 SITE 1 AC4 3 ARG A 748 TRP A 790 ARG A 823 SITE 1 AC5 5 ARG A 678 ARG B 678 ASN B 753 VAL B 757 SITE 2 AC5 5 LYS B 759 SITE 1 AC6 4 TRP B 790 ARG B 823 HOH B1009 HOH B1088 SITE 1 AC7 14 ALA B 649 LYS B 651 GLU B 668 THR B 697 SITE 2 AC7 14 GLU B 698 MET B 700 GLU B 701 ASN B 702 SITE 3 AC7 14 ALA B 704 LEU B 751 VAL B 752 ASP B 762 SITE 4 AC7 14 HOH B1048 HOH B1080 CRYST1 102.200 102.200 157.550 90.00 90.00 120.00 P 31 2 1 12 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 0.009785 0.005649 0.000000 0.00000 SCALE2 0.000000 0.011298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006347 0.00000