HEADER TRANSFERASE/TRANSFERASE INHIBITOR 08-JUN-98 1BHF TITLE P56LCK SH2 DOMAIN INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-LYMPHOCYTE-SPECIFIC PROTEIN TYROSINE KINASE P56LCK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN; COMPND 5 EC: 2.7.1.112; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: INHIBITOR ACE-IPA-GLU-GLU-ILE; COMPND 9 CHAIN: I; 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 KEYWDS SH2 DOMAIN, PHOSPHORYLATION, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.TONG,T.C.WARREN,S.LUKAS,J.SCHEMBRI-KING,R.BETAGERI,J.R.PROUDFOOT, AUTHOR 2 S.JAKES REVDAT 5 13-NOV-24 1BHF 1 REMARK REVDAT 4 05-JUN-24 1BHF 1 DBREF LINK REVDAT 3 13-JUL-11 1BHF 1 VERSN REVDAT 2 24-FEB-09 1BHF 1 VERSN REVDAT 1 21-OCT-98 1BHF 0 JRNL AUTH L.TONG,T.C.WARREN,S.LUKAS,J.SCHEMBRI-KING,R.BETAGERI, JRNL AUTH 2 J.R.PROUDFOOT,S.JAKES JRNL TITL CARBOXYMETHYL-PHENYLALANINE AS A REPLACEMENT FOR JRNL TITL 2 PHOSPHOTYROSINE IN SH2 DOMAIN BINDING. JRNL REF J.BIOL.CHEM. V. 273 20238 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9685372 JRNL DOI 10.1074/JBC.273.32.20238 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 7883 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) : 0.226 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 : 891 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 107 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.700 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 1BHF 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_1000171761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-95 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU REMARK 200 DATA SCALING SOFTWARE : RIGAKU REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8151 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 40.35000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 13.05000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.60000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE ACE-IPA-GLU-GLU-ILE IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ACE-IPA-GLU-GLU-ILE REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 ALA A 119 REMARK 465 ASN A 120 REMARK 465 SER A 121 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 123 78.48 8.28 REMARK 500 PHE A 129 78.01 -112.79 REMARK 500 THR A 147 -156.69 -143.57 REMARK 500 ILE A 197 112.96 -166.90 REMARK 500 SER A 221 -94.13 -109.23 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 CHAIN I OF INHIBITOR ACE-IPA REMARK 800 -GLU-GLU-ILE DBREF 1BHF A 119 226 UNP P06239 LCK_HUMAN 118 225 DBREF 1BHF I 251 255 PDB 1BHF 1BHF 251 255 SEQRES 1 A 108 ALA ASN SER LEU GLU PRO GLU PRO TRP PHE PHE LYS ASN SEQRES 2 A 108 LEU SER ARG LYS ASP ALA GLU ARG GLN LEU LEU ALA PRO SEQRES 3 A 108 GLY ASN THR HIS GLY SER PHE LEU ILE ARG GLU SER GLU SEQRES 4 A 108 SER THR ALA GLY SER PHE SER LEU SER VAL ARG ASP PHE SEQRES 5 A 108 ASP GLN ASN GLN GLY GLU VAL VAL LYS HIS TYR LYS ILE SEQRES 6 A 108 ARG ASN LEU ASP ASN GLY GLY PHE TYR ILE SER PRO ARG SEQRES 7 A 108 ILE THR PHE PRO GLY LEU HIS GLU LEU VAL ARG HIS TYR SEQRES 8 A 108 THR ASN ALA SER ASP GLY LEU CYS THR ARG LEU SER ARG SEQRES 9 A 108 PRO CYS GLN THR SEQRES 1 I 5 ACE 1PA GLU GLU ILE MODRES 1BHF 1PA I 252 PHE 4-(CARBOXYMETHYL)-L-PHENYLALANINE HET ACE I 251 3 HET 1PA I 252 15 HETNAM ACE ACETYL GROUP HETNAM 1PA 4-(CARBOXYMETHYL)-L-PHENYLALANINE HETSYN 1PA P-(CARBOXYMETHYL)PHENYLALANINE FORMUL 2 ACE C2 H4 O FORMUL 2 1PA C11 H13 N O4 FORMUL 3 HOH *107(H2 O) HELIX 1 1 ARG A 134 LEU A 141 1 8 HELIX 2 2 LEU A 202 ASN A 211 1 10 SHEET 1 A 3 PHE A 151 GLU A 155 0 SHEET 2 A 3 PHE A 163 PHE A 170 -1 N SER A 166 O LEU A 152 SHEET 3 A 3 GLU A 176 ILE A 183 -1 N ILE A 183 O PHE A 163 SHEET 1 B 2 PHE A 191 SER A 194 0 SHEET 2 B 2 ILE A 197 PHE A 199 -1 N PHE A 199 O PHE A 191 LINK C ACE I 251 N 1PA I 252 1555 1555 1.34 LINK C 1PA I 252 N GLU I 253 1555 1555 1.32 SITE 1 AC1 35 ARG A 134 ARG A 154 SER A 156 GLU A 157 SITE 2 AC1 35 SER A 158 SER A 164 LYS A 179 HIS A 180 SITE 3 AC1 35 TYR A 181 LYS A 182 TYR A 209 ALA A 212 SITE 4 AC1 35 SER A 213 ASP A 214 GLY A 215 LEU A 216 SITE 5 AC1 35 CYS A 217 THR A 218 ARG A 219 SER A 221 SITE 6 AC1 35 HOH A 301 HOH A 314 HOH A 364 HOH A 374 SITE 7 AC1 35 HOH A 377 HOH I 302 HOH I 308 HOH I 310 SITE 8 AC1 35 HOH I 313 HOH I 315 HOH I 325 HOH I 326 SITE 9 AC1 35 HOH I 327 HOH I 332 HOH I 363 CRYST1 80.700 45.200 26.100 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 0.012392 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038314 0.00000