HEADER TRANSFERASE 21-OCT-10 2XUU TITLE CRYSTAL STRUCTURE OF A DAP-KINASE 1 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC AND AUTOINHIBITORY DOMAIN, RESIDUES 1-334; COMPND 5 SYNONYM: DAP KINASE 1; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PETM14 KEYWDS TRANSFERASE, ATP-BINDING, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR I.DE DIEGO,J.KUPER,F.LEHMANN,M.WILMANNS REVDAT 4 20-DEC-23 2XUU 1 REMARK LINK REVDAT 3 05-MAR-14 2XUU 1 JRNL REVDAT 2 05-FEB-14 2XUU 1 JRNL REMARK REVDAT 1 02-NOV-11 2XUU 0 JRNL AUTH K.TEMMERMAN,I.DE DIEGO,V.POGENBERG,B.SIMON,W.JONKO,X.LI, JRNL AUTH 2 M.WILMANNS JRNL TITL A PEF/Y SUBSTRATE RECOGNITION AND SIGNATURE MOTIF PLAYS A JRNL TITL 2 CRITICAL ROLE IN DAPK-RELATED KINASE ACTIVITY. JRNL REF CHEM.BIOL. V. 21 264 2014 JRNL REFN ISSN 1074-5521 JRNL PMID 24440081 JRNL DOI 10.1016/J.CHEMBIOL.2013.12.008 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32678 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1736 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2397 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2411 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56000 REMARK 3 B22 (A**2) : -0.78000 REMARK 3 B33 (A**2) : 1.34000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.720 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2500 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3383 ; 2.009 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 6.055 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;34.809 ;24.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 450 ;16.442 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;20.884 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 375 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1853 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1500 ; 1.323 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2424 ; 2.294 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1000 ; 3.590 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 959 ; 5.774 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES 2-302 ARE MODELLED.SIDE CHAINS RESIDUES R48, REMARK 3 R156, K261 AND R302 DISORDERED AND REMOVED FROM MODEL. REMARK 4 REMARK 4 2XUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1290045071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI (111) CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 2W4K REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LISO4 0.1 M BIS-TRIS PH 5.5 25% REMARK 280 PEG 4000 0.002% NAN3 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 24.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.17000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.21500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.17000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.21500 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 182 TO ALA 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 1 REMARK 465 LYS A 303 REMARK 465 LYS A 304 REMARK 465 TRP A 305 REMARK 465 LYS A 306 REMARK 465 GLN A 307 REMARK 465 SER A 308 REMARK 465 VAL A 309 REMARK 465 ARG A 310 REMARK 465 LEU A 311 REMARK 465 ILE A 312 REMARK 465 SER A 313 REMARK 465 LEU A 314 REMARK 465 CYS A 315 REMARK 465 GLN A 316 REMARK 465 ARG A 317 REMARK 465 LEU A 318 REMARK 465 SER A 319 REMARK 465 ARG A 320 REMARK 465 SER A 321 REMARK 465 PHE A 322 REMARK 465 LEU A 323 REMARK 465 SER A 324 REMARK 465 ARG A 325 REMARK 465 SER A 326 REMARK 465 ASN A 327 REMARK 465 MET A 328 REMARK 465 SER A 329 REMARK 465 VAL A 330 REMARK 465 ALA A 331 REMARK 465 ARG A 332 REMARK 465 SER A 333 REMARK 465 ASP A 334 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 48 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 156 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 ARG A 302 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASN A 125 O HOH A 2213 1.90 REMARK 500 O ASN A 172 O HOH A 2269 1.92 REMARK 500 OD1 ASN A 176 O HOH A 2277 2.02 REMARK 500 N PHE A 24 O HOH A 2049 2.13 REMARK 500 O HOH A 2058 O HOH A 2061 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2289 O HOH A 2379 3554 1.12 REMARK 500 O HOH A 2291 O HOH A 2388 3554 1.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 171 N GLY A 171 CA 0.109 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 88 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 GLY A 171 C - N - CA ANGL. DEV. = -21.0 DEGREES REMARK 500 ARG A 253 CG - CD - NE ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = -4.5 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 ARG A 48 -62.99 102.63 REMARK 500 ASP A 139 42.84 -146.35 REMARK 500 ASP A 161 81.82 67.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2050 DISTANCE = 6.63 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ADENOSINE-5'-DIPHOSPHATE (ADP): ADDITIVE AT 5 MM REMARK 600 MAGNESIUM ION (MG): ADDITIVE AT 5MM REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 161 OD2 REMARK 620 2 ADP A1303 O2B 97.3 REMARK 620 3 ADP A1303 O1A 89.5 88.4 REMARK 620 4 HOH A2223 O 85.7 92.0 175.2 REMARK 620 5 HOH A2234 O 95.3 165.4 84.2 96.3 REMARK 620 6 HOH A2402 O 172.7 81.3 97.6 87.2 87.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JKK RELATED DB: PDB REMARK 900 2.4A X-RAY STRUCTURE OF TERNARY COMPLEX OF A CATALYTICDOMAIN OF REMARK 900 DEATH-ASSOCIATED PROTEIN KINASE WITH ATPANALOGUE AND MG. REMARK 900 RELATED ID: 2YAK RELATED DB: PDB REMARK 900 STRUCTURE OF DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) IN COMPLEX REMARK 900 WITH A RUTHENIUM OCTASPORINE LIGAND (OSV) REMARK 900 RELATED ID: 1P4F RELATED DB: PDB REMARK 900 DEATH ASSOCIATED PROTEIN KINASE CATALYTIC DOMAIN WITH REMARK 900 BOUNDINHIBITOR FRAGMENT REMARK 900 RELATED ID: 2Y0A RELATED DB: PDB REMARK 900 STRUCTURE OF DAPK1 CONSTRUCT RESIDUES 1-304 REMARK 900 RELATED ID: 2W4J RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A DAP-KINASE 2-277 REMARK 900 RELATED ID: 2X0G RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX REMARK 900 RELATED ID: 2Y4V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINASE- REMARK 900 1 MUTANT (W305Y) PEPTIDE REMARK 900 RELATED ID: 3ZXT RELATED DB: PDB REMARK 900 DIMERIC STRUCTURE OF DAPK-1 CATALYTIC DOMAIN IN COMPLEX WITH AMPPCP- REMARK 900 MG REMARK 900 RELATED ID: 2W4K RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A DAP-KINASE 2-302 REMARK 900 RELATED ID: 1JKT RELATED DB: PDB REMARK 900 TETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH -ASSOCIATED REMARK 900 PROTEIN KINASE REMARK 900 RELATED ID: 1IG1 RELATED DB: PDB REMARK 900 1.8A X-RAY STRUCTURE OF TERNARY COMPLEX OF A CATALYTICDOMAIN OF REMARK 900 DEATH-ASSOCIATED PROTEIN KINASE WITH ATPANALOGUE AND MN. REMARK 900 RELATED ID: 1JKS RELATED DB: PDB REMARK 900 1.5A X-RAY STRUCTURE OF APO FORM OF A CATALYTIC DOMAIN OFDEATH- REMARK 900 ASSOCIATED PROTEIN KINASE REMARK 900 RELATED ID: 1JKL RELATED DB: PDB REMARK 900 1.6A X-RAY STRUCTURE OF BINARY COMPLEX OF A CATALYTICDOMAIN OF REMARK 900 DEATH-ASSOCIATED PROTEIN KINASE WITH ATP ANALOGUE REMARK 900 RELATED ID: 2XZS RELATED DB: PDB REMARK 900 DEATH ASSOCIATED PROTEIN KINASE 1 RESIDUES 1-312 REMARK 900 RELATED ID: 2Y4P RELATED DB: PDB REMARK 900 DIMERIC STRUCTURE OF DAPK-1 CATALYTIC DOMAIN REMARK 900 RELATED ID: 4B4L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ARD DAP-KINASE 1 MUTANT DBREF 2XUU A 1 334 UNP P53355 DAPK1_HUMAN 1 334 SEQADV 2XUU ALA A 182 UNP P53355 GLU 182 ENGINEERED MUTATION SEQRES 1 A 334 MET THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 A 334 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 A 334 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 A 334 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 A 334 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 A 334 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 A 334 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 A 334 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 A 334 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 A 334 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 A 334 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 A 334 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 A 334 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 A 334 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO ALA SEQRES 15 A 334 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 A 334 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 A 334 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 A 334 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 A 334 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 A 334 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 A 334 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 A 334 TRP ILE LYS PRO LYS ASP THR GLN GLN ALA LEU SER ARG SEQRES 23 A 334 LYS ALA SER ALA VAL ASN MET GLU LYS PHE LYS LYS PHE SEQRES 24 A 334 ALA ALA ARG LYS LYS TRP LYS GLN SER VAL ARG LEU ILE SEQRES 25 A 334 SER LEU CYS GLN ARG LEU SER ARG SER PHE LEU SER ARG SEQRES 26 A 334 SER ASN MET SER VAL ALA ARG SER ASP HET ADP A1303 27 HET SO4 A1304 5 HET SO4 A1305 5 HET SO4 A1306 5 HET MG A1307 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 MG MG 2+ FORMUL 7 HOH *408(H2 O) HELIX 1 1 ASN A 8 ASP A 11 5 4 HELIX 2 2 SER A 57 ILE A 71 1 15 HELIX 3 3 GLU A 100 ALA A 106 1 7 HELIX 4 4 THR A 112 LEU A 133 1 22 HELIX 5 5 LYS A 141 GLU A 143 5 3 HELIX 6 6 THR A 180 VAL A 184 5 5 HELIX 7 7 ALA A 185 ASN A 190 1 6 HELIX 8 8 LEU A 196 GLY A 213 1 18 HELIX 9 9 THR A 221 ALA A 231 1 11 HELIX 10 10 GLU A 237 SER A 242 1 6 HELIX 11 11 SER A 245 LEU A 256 1 12 HELIX 12 12 ASP A 259 ARG A 263 5 5 HELIX 13 13 THR A 265 HIS A 272 1 8 HELIX 14 14 ASP A 279 SER A 289 1 11 HELIX 15 15 ASN A 292 ALA A 301 1 10 SHEET 1 AA 5 TYR A 13 GLY A 22 0 SHEET 2 AA 5 ALA A 25 GLU A 32 -1 O ALA A 25 N GLY A 22 SHEET 3 AA 5 GLN A 38 LYS A 45 -1 O TYR A 39 N CYS A 30 SHEET 4 AA 5 ASP A 88 GLU A 94 -1 O VAL A 89 N ILE A 44 SHEET 5 AA 5 LEU A 79 GLU A 84 -1 N HIS A 80 O ILE A 92 SHEET 1 AB 2 ILE A 135 ALA A 136 0 SHEET 2 AB 2 HIS A 166 LYS A 167 -1 O HIS A 166 N ALA A 136 SHEET 1 AC 2 ILE A 145 LEU A 147 0 SHEET 2 AC 2 ILE A 157 ILE A 159 -1 O LYS A 158 N MET A 146 LINK OD2 ASP A 161 MG MG A1307 1555 1555 2.18 LINK O2B ADP A1303 MG MG A1307 1555 1555 2.11 LINK O1A ADP A1303 MG MG A1307 1555 1555 2.04 LINK MG MG A1307 O HOH A2223 1555 1555 2.24 LINK MG MG A1307 O HOH A2234 1555 1555 2.08 LINK MG MG A1307 O HOH A2402 1555 1555 2.22 SITE 1 AC1 19 GLY A 20 SER A 21 GLY A 22 VAL A 27 SITE 2 AC1 19 LYS A 42 GLU A 94 VAL A 96 ILE A 160 SITE 3 AC1 19 ASP A 161 MG A1307 HOH A2048 HOH A2121 SITE 4 AC1 19 HOH A2232 HOH A2234 HOH A2398 HOH A2400 SITE 5 AC1 19 HOH A2401 HOH A2402 HOH A2403 SITE 1 AC2 8 ARG A 47 LYS A 50 SER A 57 ARG A 58 SITE 2 AC2 8 HOH A2404 HOH A2405 HOH A2406 HOH A2407 SITE 1 AC3 4 ARG A 47 LYS A 249 ARG A 253 HOH A2106 SITE 1 AC4 7 ARG A 150 ASN A 151 HOH A2174 HOH A2175 SITE 2 AC4 7 HOH A2241 HOH A2351 HOH A2408 SITE 1 AC5 5 ASP A 161 ADP A1303 HOH A2223 HOH A2234 SITE 2 AC5 5 HOH A2402 CRYST1 49.740 84.430 86.340 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 0.020105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011582 0.00000