HEADER TRANSFERASE/TRANSFERASE INHIBITOR 03-FEB-15 4XZ1 TITLE ZAP-70-TSH2:COMPOUND-B ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE ZAP-70; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 70 KDA ZETA-CHAIN ASSOCIATED PROTEIN,SYK-RELATED TYROSINE COMPND 5 KINASE; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DOUBLY PHOSPHORYLATED ITAM PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 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: ZAP70, SRK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS TYROSINE KINASE, CYSTEINE ADDUCT, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.BARROS,J.KURIYAN,J.A.WINGER,P.R.VISPERAS REVDAT 6 16-OCT-24 4XZ1 1 REMARK REVDAT 5 15-NOV-23 4XZ1 1 REMARK REVDAT 4 27-SEP-23 4XZ1 1 REMARK REVDAT 3 11-DEC-19 4XZ1 1 REMARK REVDAT 2 13-SEP-17 4XZ1 1 SOURCE REMARK REVDAT 1 29-JUL-15 4XZ1 0 JRNL AUTH P.R.VISPERAS,J.A.WINGER,T.M.HORTON,N.H.SHAH,D.J.AUM,A.TAO, JRNL AUTH 2 T.BARROS,Q.YAN,C.G.WILSON,M.R.ARKIN,A.WEISS,J.KURIYAN JRNL TITL MODIFICATION BY COVALENT REACTION OR OXIDATION OF CYSTEINE JRNL TITL 2 RESIDUES IN THE TANDEM-SH2 DOMAINS OF ZAP-70 AND SYK CAN JRNL TITL 3 BLOCK PHOSPHOPEPTIDE BINDING. JRNL REF BIOCHEM. J. V. 465 149 2015 JRNL REFN ESSN 1470-8728 JRNL PMID 25287889 JRNL DOI 10.1042/BJ20140793 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 7623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 370 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.8965 - 4.0380 1.00 2437 138 0.2013 0.2555 REMARK 3 2 4.0380 - 3.2053 1.00 2426 121 0.2142 0.2602 REMARK 3 3 3.2053 - 2.8001 1.00 2390 111 0.2623 0.3487 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.640 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2251 REMARK 3 ANGLE : 0.687 3050 REMARK 3 CHIRALITY : 0.027 316 REMARK 3 PLANARITY : 0.003 396 REMARK 3 DIHEDRAL : 13.668 844 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4XZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000206553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.989999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7638 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.75900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 2OQ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, CALCIUM CHLORIDE, MES, TCEP, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.55250 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 257 REMARK 465 SER A 258 REMARK 465 ALA A 259 REMARK 465 CYS B 299 REMARK 465 GLY B 300 REMARK 465 ASN B 301 REMARK 465 GLN B 302 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 GLN A 145 37.92 -96.07 REMARK 500 PRO A 147 -66.31 -102.69 REMARK 500 SER A 179 87.37 -68.37 REMARK 500 GLN A 195 -61.18 67.87 REMARK 500 LYS A 206 -54.82 -134.13 REMARK 500 ALA A 218 -25.25 106.99 REMARK 500 LYS A 251 -67.62 -138.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 217 ALA A 218 -144.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 COMPOUND B IS 2-[(7-CHLORO-4-NITRO-2,1,3-BENZOXADIAZOL-5-YL)AMINO] REMARK 600 ETHANOL. ATOM CAL OF 4N6 A 301 COVALENTLY LINKED TO SG ATOM OF CYS REMARK 600 A 78 IN THIS STRUCTURE. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4N6 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XZ0 RELATED DB: PDB REMARK 900 ZAP-70-TSH2:COMPOUND-A COMPLEX DBREF 4XZ1 A 1 259 UNP P43403 ZAP70_HUMAN 1 259 DBREF 4XZ1 B 299 319 PDB 4XZ1 4XZ1 299 319 SEQADV 4XZ1 GLY A -2 UNP P43403 EXPRESSION TAG SEQADV 4XZ1 PRO A -1 UNP P43403 EXPRESSION TAG SEQADV 4XZ1 HIS A 0 UNP P43403 EXPRESSION TAG SEQADV 4XZ1 SER A 117 UNP P43403 CYS 117 ENGINEERED MUTATION SEQRES 1 A 262 GLY PRO HIS MET PRO ASP PRO ALA ALA HIS LEU PRO PHE SEQRES 2 A 262 PHE TYR GLY SER ILE SER ARG ALA GLU ALA GLU GLU HIS SEQRES 3 A 262 LEU LYS LEU ALA GLY MET ALA ASP GLY LEU PHE LEU LEU SEQRES 4 A 262 ARG GLN CYS LEU ARG SER LEU GLY GLY TYR VAL LEU SER SEQRES 5 A 262 LEU VAL HIS ASP VAL ARG PHE HIS HIS PHE PRO ILE GLU SEQRES 6 A 262 ARG GLN LEU ASN GLY THR TYR ALA ILE ALA GLY GLY LYS SEQRES 7 A 262 ALA HIS CYS GLY PRO ALA GLU LEU CYS GLU PHE TYR SER SEQRES 8 A 262 ARG ASP PRO ASP GLY LEU PRO CYS ASN LEU ARG LYS PRO SEQRES 9 A 262 CYS ASN ARG PRO SER GLY LEU GLU PRO GLN PRO GLY VAL SEQRES 10 A 262 PHE ASP SER LEU ARG ASP ALA MET VAL ARG ASP TYR VAL SEQRES 11 A 262 ARG GLN THR TRP LYS LEU GLU GLY GLU ALA LEU GLU GLN SEQRES 12 A 262 ALA ILE ILE SER GLN ALA PRO GLN VAL GLU LYS LEU ILE SEQRES 13 A 262 ALA THR THR ALA HIS GLU ARG MET PRO TRP TYR HIS SER SEQRES 14 A 262 SER LEU THR ARG GLU GLU ALA GLU ARG LYS LEU TYR SER SEQRES 15 A 262 GLY ALA GLN THR ASP GLY LYS PHE LEU LEU ARG PRO ARG SEQRES 16 A 262 LYS GLU GLN GLY THR TYR ALA LEU SER LEU ILE TYR GLY SEQRES 17 A 262 LYS THR VAL TYR HIS TYR LEU ILE SER GLN ASP LYS ALA SEQRES 18 A 262 GLY LYS TYR CYS ILE PRO GLU GLY THR LYS PHE ASP THR SEQRES 19 A 262 LEU TRP GLN LEU VAL GLU TYR LEU LYS LEU LYS ALA ASP SEQRES 20 A 262 GLY LEU ILE TYR CYS LEU LYS GLU ALA CYS PRO ASN SER SEQRES 21 A 262 SER ALA SEQRES 1 B 21 CYS GLY ASN GLN LEU PTR ASN GLU LEU ASN LEU GLY ARG SEQRES 2 B 21 ARG GLU GLU PTR ASP VAL LEU ASP HET PTR B 304 23 HET PTR B 315 23 HET 4N6 A 301 23 HETNAM PTR O-PHOSPHOTYROSINE HETNAM 4N6 2-[(7-CHLORO-4-NITRO-2,1,3-BENZOXADIAZOL-5-YL) HETNAM 2 4N6 AMINO]ETHANOL HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR 2(C9 H12 N O6 P) FORMUL 3 4N6 C8 H7 CL N4 O4 HELIX 1 AA1 SER A 16 ALA A 27 1 12 HELIX 2 AA2 GLY A 79 SER A 88 1 10 HELIX 3 AA3 GLY A 113 LYS A 132 1 20 HELIX 4 AA4 GLU A 134 GLN A 145 1 12 HELIX 5 AA5 GLN A 148 THR A 156 1 9 HELIX 6 AA6 ALA A 157 MET A 161 5 5 HELIX 7 AA7 THR A 169 SER A 179 1 11 HELIX 8 AA8 THR A 231 LYS A 242 1 12 SHEET 1 AA1 5 TYR A 69 ILE A 71 0 SHEET 2 AA1 5 ARG A 55 ARG A 63 -1 N GLU A 62 O ALA A 70 SHEET 3 AA1 5 TYR A 46 HIS A 52 -1 N TYR A 46 O ILE A 61 SHEET 4 AA1 5 LEU A 33 GLN A 38 -1 N ARG A 37 O VAL A 47 SHEET 5 AA1 5 LYS A 100 PRO A 101 1 O LYS A 100 N PHE A 34 SHEET 1 AA2 5 PHE A 187 PRO A 191 0 SHEET 2 AA2 5 THR A 197 TYR A 204 -1 O ALA A 199 N ARG A 190 SHEET 3 AA2 5 THR A 207 ASP A 216 -1 O ILE A 213 N TYR A 198 SHEET 4 AA2 5 LYS A 220 CYS A 222 -1 O CYS A 222 N SER A 214 SHEET 5 AA2 5 LYS A 228 PHE A 229 -1 O PHE A 229 N TYR A 221 LINK SG CYS A 78 CAL 4N6 A 301 1555 1555 1.77 LINK C LEU B 303 N PTR B 304 1555 1555 1.33 LINK C PTR B 304 N ASN B 305 1555 1555 1.33 LINK C GLU B 314 N PTR B 315 1555 1555 1.33 LINK C PTR B 315 N ASP B 316 1555 1555 1.33 SITE 1 AC1 4 ASN A 66 GLY A 67 THR A 68 CYS A 78 CRYST1 52.944 61.105 53.451 90.00 116.37 90.00 P 1 21 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 0.018888 0.000000 0.009363 0.00000 SCALE2 0.000000 0.016365 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020881 0.00000