PDB Short entry for 1O46 HEADER SIGNALING PROTEIN 15-JUN-03 1O46 TITLE CRYSTAL STRUCTURE OF SH2 IN COMPLEX WITH RU90395. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN; COMPND 5 SYNONYM: P60-SRC, C-SRC; COMPND 6 EC: 2.7.1.112; COMPND 7 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: SRC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SH2 DOMAIN FRAGMENT APPROACH, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.LANGE,P.LOENZE,A.LIESUM REVDAT 4 16-AUG-23 1O46 1 REMARK REVDAT 3 10-DEC-14 1O46 1 SOURCE CRYST1 REMARK VERSN REVDAT 2 24-FEB-09 1O46 1 VERSN REVDAT 1 17-FEB-04 1O46 0 JRNL AUTH G.LANGE,D.LESUISSE,P.DEPREZ,B.SCHOOT,P.LOENZE,D.BENARD, JRNL AUTH 2 J.P.MARQUETTE,P.BROTO,E.SARUBBI,E.MANDINE JRNL TITL REQUIREMENTS FOR SPECIFIC BINDING OF LOW AFFINITY INHIBITOR JRNL TITL 2 FRAGMENTS TO THE SH2 DOMAIN OF (PP60)SRC ARE IDENTICAL TO JRNL TITL 3 THOSE FOR HIGH AFFINITY BINDING OF FULL LENGTH INHIBITORS. JRNL REF J.MED.CHEM. V. 46 5184 2003 JRNL REFN ISSN 0022-2623 JRNL PMID 14613321 JRNL DOI 10.1021/JM020970S REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 6879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 855 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1O46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000001781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 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 : ELLIOTT GX-21 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6879 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: PDB ENTRY 1SHD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 13.29350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.09400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.27700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.09400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.29350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.27700 REMARK 290 SMTRY3 4 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 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 SER A 107 REMARK 465 LYS A 108 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 14 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 GLU A 25 CA - CB - CG ANGL. DEV. = -25.0 DEGREES REMARK 500 ASP A 51 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 LYS A 54 CB - CA - C ANGL. DEV. = -13.5 DEGREES REMARK 500 LYS A 59 CA - CB - CG ANGL. DEV. = -13.7 DEGREES REMARK 500 ASP A 67 CB - CA - C ANGL. DEV. = 14.9 DEGREES REMARK 500 GLN A 83 CA - CB - CG ANGL. DEV. = -20.7 DEGREES REMARK 500 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 CYS A 104 CB - CA - C ANGL. DEV. = -14.7 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 LEU A 22 36.49 -79.83 REMARK 500 ASP A 94 -118.94 56.75 REMARK 500 THR A 101 -64.61 -107.75 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 903 A 300 DBREF 1O46 A 1 108 UNP P12931 SRC_HUMAN 144 251 SEQRES 1 A 108 SER ILE GLN ALA GLU GLU TRP TYR PHE GLY LYS ILE THR SEQRES 2 A 108 ARG ARG GLU SER GLU ARG LEU LEU LEU ASN ALA GLU ASN SEQRES 3 A 108 PRO ARG GLY THR PHE LEU VAL ARG GLU SER GLU THR THR SEQRES 4 A 108 LYS GLY ALA TYR CYS LEU SER VAL SER ASP PHE ASP ASN SEQRES 5 A 108 ALA LYS GLY LEU ASN VAL LYS HIS TYR LYS ILE ARG LYS SEQRES 6 A 108 LEU ASP SER GLY GLY PHE TYR ILE THR SER ARG THR GLN SEQRES 7 A 108 PHE ASN SER LEU GLN GLN LEU VAL ALA TYR TYR SER LYS SEQRES 8 A 108 HIS ALA ASP GLY LEU CYS HIS ARG LEU THR THR VAL CYS SEQRES 9 A 108 PRO THR SER LYS HET 903 A 300 48 HETNAM 903 2-{4-[2-ACETYLAMINO-2-(1-BIPHENYL-4-YLMETHYL-2-OXO- HETNAM 2 903 AZEPAN-3-YLCARBAMOYL)-ETHYL]-2-METHOXYCARBONYL- HETNAM 3 903 PHENYL}-2-FLUORO-MALONIC ACID HETSYN 903 RU90395 FORMUL 2 903 C35 H36 F N3 O9 FORMUL 3 HOH *142(H2 O) HELIX 1 1 SER A 1 GLU A 5 5 5 HELIX 2 2 THR A 13 LEU A 22 1 10 HELIX 3 3 SER A 81 HIS A 92 1 12 SHEET 1 A 6 TYR A 8 GLY A 10 0 SHEET 2 A 6 PHE A 31 GLU A 35 1 O GLU A 35 N GLY A 10 SHEET 3 A 6 TYR A 43 ASP A 51 -1 O CYS A 44 N ARG A 34 SHEET 4 A 6 GLY A 55 LYS A 65 -1 O ILE A 63 N TYR A 43 SHEET 5 A 6 PHE A 71 TYR A 72 -1 O TYR A 72 N ARG A 64 SHEET 6 A 6 GLN A 78 PHE A 79 -1 O PHE A 79 N PHE A 71 SITE 1 AC1 17 ARG A 14 ARG A 34 SER A 36 GLU A 37 SITE 2 AC1 17 THR A 38 CYS A 44 HIS A 60 LYS A 62 SITE 3 AC1 17 GLY A 95 LEU A 96 VAL A 103 PRO A 105 SITE 4 AC1 17 THR A 106 HOH A 337 HOH A 344 HOH A 377 SITE 5 AC1 17 HOH A 421 CRYST1 26.587 58.554 64.188 90.00 90.00 90.00 P 21 21 21 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 0.037612 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015579 0.00000