HEADER TRANSFERASE/PEPTIDE 06-SEP-95 1CWE TITLE HUMAN P56LCK TYROSINE KINASE COMPLEXED WITH PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: P56LCK TYROSINE KINASE; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PHOSPHOTYROSINE RECOGNITION DOMAIN SH2; COMPND 5 EC: 2.7.1.112; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PHOSPHOPEPTIDE ACQ-PMP-GLU-GLU-ILE-PRO; COMPND 9 CHAIN: B, D; COMPND 10 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: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 OTHER_DETAILS: SYNTHESIZED USING STEP-WISE NA-FMOC STRATEGY KEYWDS PHOSPHOTRANSFERASE, TRANSFERASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.MIKOL REVDAT 5 05-JUN-24 1CWE 1 LINK REVDAT 4 17-AUG-11 1CWE 1 SOURCE REVDAT 3 03-AUG-11 1CWE 1 COMPND HEADER KEYWDS SEQRES REVDAT 2 24-FEB-09 1CWE 1 VERSN REVDAT 1 07-DEC-96 1CWE 0 JRNL AUTH V.MIKOL,G.BAUMANN,T.H.KELLER,U.MANNING,M.G.ZURINI JRNL TITL THE CRYSTAL STRUCTURES OF THE SH2 DOMAIN OF P56LCK COMPLEXED JRNL TITL 2 WITH TWO PHOSPHOPEPTIDES SUGGEST A GATED PEPTIDE BINDING JRNL TITL 3 SITE. JRNL REF J.MOL.BIOL. V. 246 344 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7532720 JRNL DOI 10.1006/JMBI.1994.0089 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 : 1677 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 216 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.800 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 1CWE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10015 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 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 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 300 REMARK: THE COMPLEX CRYSTALLIZES AS A DIMER IN WHICH THE TWO REMARK 300 MOLECULES ARE RELATED BY APPROXIMATE TWO-FOLD SYMMETRY. REMARK 300 THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A REMARK 300 AND C. RESIDUES 201 TO 205 COMPRISE THE PHOSPHOPEPTIDE. REMARK 300 THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN IDENTIFIERS B REMARK 300 AND D. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ACE B 200 REMARK 465 ACE D 200 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 100 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 100 CB CG CD NE CZ NH1 NH2 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 LEU A 30 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 PRO C 22 C - N - CA ANGL. DEV. = 10.5 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 SER A 4 -46.97 -170.47 REMARK 500 ASP A 92 52.56 39.29 REMARK 500 SER A 99 -120.88 -79.74 REMARK 500 SER C 4 -89.93 27.86 REMARK 500 TYR C 70 145.99 -175.45 REMARK 500 ALA C 90 139.46 -175.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 54 10.16 REMARK 500 ILE A 75 10.65 REMARK 500 SER C 4 -10.28 REMARK 500 ILE C 61 10.73 REMARK 500 THR C 96 10.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE REGION BETWEEN RESIDUES 3 AND 100 CORRESPONDS TO THE REMARK 999 REGION OF THE P56LCK TYROSINE KINASE BETWEEN RESIDUES 124 REMARK 999 AND 221. DBREF 1CWE A 5 100 UNP P06239 LCK_HUMAN 126 221 DBREF 1CWE C 5 100 UNP P06239 LCK_HUMAN 126 221 DBREF 1CWE B 201 206 PDB 1CWE 1CWE 201 206 DBREF 1CWE D 201 206 PDB 1CWE 1CWE 201 206 SEQRES 1 A 98 GLY SER TRP PHE PHE LYS ASN LEU SER ARG LYS ASP ALA SEQRES 2 A 98 GLU ARG GLN LEU LEU ALA PRO GLY ASN THR HIS GLY SER SEQRES 3 A 98 PHE LEU ILE ARG GLU SER GLU SER THR ALA GLY SER PHE SEQRES 4 A 98 SER LEU SER VAL ARG ASP PHE ASP GLN ASN GLN GLY GLU SEQRES 5 A 98 VAL VAL LYS HIS TYR LYS ILE ARG ASN LEU ASP ASN GLY SEQRES 6 A 98 GLY PHE TYR ILE SER PRO ARG ILE THR PHE PRO GLY LEU SEQRES 7 A 98 HIS GLU LEU VAL ARG HIS TYR THR ASN ALA SER ASP GLY SEQRES 8 A 98 LEU CYS THR ARG LEU SER ARG SEQRES 1 B 7 ACE GLN PM3 GLU GLU ILE PRO SEQRES 1 C 98 GLY SER TRP PHE PHE LYS ASN LEU SER ARG LYS ASP ALA SEQRES 2 C 98 GLU ARG GLN LEU LEU ALA PRO GLY ASN THR HIS GLY SER SEQRES 3 C 98 PHE LEU ILE ARG GLU SER GLU SER THR ALA GLY SER PHE SEQRES 4 C 98 SER LEU SER VAL ARG ASP PHE ASP GLN ASN GLN GLY GLU SEQRES 5 C 98 VAL VAL LYS HIS TYR LYS ILE ARG ASN LEU ASP ASN GLY SEQRES 6 C 98 GLY PHE TYR ILE SER PRO ARG ILE THR PHE PRO GLY LEU SEQRES 7 C 98 HIS GLU LEU VAL ARG HIS TYR THR ASN ALA SER ASP GLY SEQRES 8 C 98 LEU CYS THR ARG LEU SER ARG SEQRES 1 D 7 ACE GLN PM3 GLU GLU ILE PRO MODRES 1CWE PM3 B 202 PHE MODRES 1CWE PM3 D 202 PHE HET PM3 B 202 16 HET PM3 D 202 16 HETNAM PM3 2-AMINO-3-(4-PHOSPHONOMETHYL-PHENYL)-PROPIONIC ACID FORMUL 2 PM3 2(C10 H14 N O5 P) FORMUL 5 HOH *216(H2 O) HELIX 1 1 ARG A 12 LEU A 19 1 8 HELIX 2 2 LEU A 80 TYR A 87 1 8 HELIX 3 3 ARG C 12 LEU C 19 1 8 HELIX 4 4 LEU C 80 THR C 88 1 9 SHEET 1 A 4 PHE A 6 LYS A 8 0 SHEET 2 A 4 PHE A 29 GLU A 33 1 N ILE A 31 O PHE A 7 SHEET 3 A 4 PHE A 41 ASP A 49 -1 N SER A 44 O LEU A 30 SHEET 4 A 4 GLY A 53 LYS A 60 -1 N TYR A 59 O LEU A 43 SHEET 1 B 4 PHE C 6 LYS C 8 0 SHEET 2 B 4 PHE C 29 GLU C 33 1 N ILE C 31 O PHE C 7 SHEET 3 B 4 PHE C 41 ASP C 49 -1 N SER C 44 O LEU C 30 SHEET 4 B 4 GLY C 53 LYS C 60 -1 N TYR C 59 O LEU C 43 LINK C GLN B 201 N PM3 B 202 1555 1555 1.35 LINK C PM3 B 202 N GLU B 203 1555 1555 1.32 LINK C GLN D 201 N PM3 D 202 1555 1555 1.34 LINK C PM3 D 202 N GLU D 203 1555 1555 1.32 CRYST1 35.170 41.840 45.520 68.71 82.94 87.36 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 0.028433 -0.001311 -0.003269 0.00000 SCALE2 0.000000 0.023926 -0.009248 0.00000 SCALE3 0.000000 0.000000 0.023732 0.00000 MTRIX1 1 -0.414900 0.440100 -0.796400 17.88140 1 MTRIX2 1 0.513200 -0.609600 -0.604200 59.77560 1 MTRIX3 1 -0.751400 -0.659300 0.027100 64.71060 1