HEADER TRANSFERASE 29-NOV-10 2XZS TITLE DEATH ASSOCIATED PROTEIN KINASE 1 RESIDUES 1-312 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH ASSOCIATED KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE CATALYTIC DOMAIN, RESIDUES 1-312; COMPND 5 SYNONYM: DAP KINASE 1; COMPND 6 EC: 2.7.11.1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PYUM6002/PET-9A KEYWDS TRANSFERASE, CALMODULIN, ESPRIT EXPDTA X-RAY DIFFRACTION AUTHOR H.YUMEREFENDI,P.J.MAS,N.DORDEVIC,A.A.MCCARTHY,D.J.HART REVDAT 5 20-DEC-23 2XZS 1 REMARK LINK REVDAT 4 22-JUN-16 2XZS 1 JRNL REVDAT 3 18-MAY-16 2XZS 1 JRNL REMARK REVDAT 2 21-NOV-12 2XZS 1 DBREF REVDAT 1 07-DEC-11 2XZS 0 JRNL AUTH B.SIMON,A.HUART,K.TEMMERMAN,J.VAHOKOSKI,H.D.T.MERTENS, JRNL AUTH 2 D.KOMADINA,J.HOFFMANN,H.YUMEREFENDI,D.I.SVERGUN,P.KURSULA, JRNL AUTH 3 C.SCHULTZ,A.A.MCCARTHY,D.J.HART,M.WILMANNS JRNL TITL DEATH-ASSOCIATED PROTEIN KINASE ACTIVITY IS REGULATED BY JRNL TITL 2 COUPLED CALCIUM/CALMODULIN BINDING TO TWO DISTINCT SITES. JRNL REF STRUCTURE V. 24 851 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27133022 JRNL DOI 10.1016/J.STR.2016.03.020 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 44470 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2346 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3015 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4656 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : 0.17000 REMARK 3 B33 (A**2) : -1.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.588 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4770 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6464 ; 1.825 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 595 ; 6.040 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;35.547 ;25.045 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 816 ;15.076 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;23.317 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 732 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3609 ; 0.010 ; 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): 2969 ; 1.101 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4766 ; 1.875 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1801 ; 3.126 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1696 ; 4.934 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 4 A 302 4 REMARK 3 1 B 4 B 302 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2249 ; 0.35 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 2249 ; 0.35 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2249 ; 1.94 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 2249 ; 1.94 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 312 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8504 -9.6393 51.7627 REMARK 3 T TENSOR REMARK 3 T11: 0.0287 T22: 0.0244 REMARK 3 T33: 0.0635 T12: -0.0018 REMARK 3 T13: 0.0124 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 0.4345 L22: 0.7351 REMARK 3 L33: 0.9640 L12: -0.2700 REMARK 3 L13: 0.1262 L23: 0.1686 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: 0.0726 S13: 0.0177 REMARK 3 S21: -0.0793 S22: -0.0205 S23: -0.0542 REMARK 3 S31: 0.0168 S32: 0.1252 S33: 0.0359 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 302 REMARK 3 ORIGIN FOR THE GROUP (A): -7.2930 -21.3326 18.3157 REMARK 3 T TENSOR REMARK 3 T11: 0.2138 T22: 0.2706 REMARK 3 T33: 0.0906 T12: 0.0359 REMARK 3 T13: -0.0074 T23: -0.0442 REMARK 3 L TENSOR REMARK 3 L11: 1.2593 L22: 0.7657 REMARK 3 L33: 2.5630 L12: 0.2688 REMARK 3 L13: 0.0264 L23: -0.2854 REMARK 3 S TENSOR REMARK 3 S11: 0.0397 S12: 0.5074 S13: 0.0377 REMARK 3 S21: -0.1937 S22: -0.0450 S23: 0.0806 REMARK 3 S31: 0.0173 S32: -0.0731 S33: 0.0052 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. REMARK 4 REMARK 4 2XZS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046242. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : TOROIDAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46826 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 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 (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 1IG1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M SODIUM CACODYLATE, PH 6.5 AND 10% PEG 8000 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 24.80500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 1 REMARK 465 THR A 2 REMARK 465 VAL A 3 REMARK 465 ARG A 48 REMARK 465 THR A 49 REMARK 465 LYS A 50 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 GLY B 1 REMARK 465 THR B 2 REMARK 465 VAL B 3 REMARK 465 ARG B 47 REMARK 465 ARG B 48 REMARK 465 THR B 49 REMARK 465 LYS B 50 REMARK 465 SER B 51 REMARK 465 SER B 52 REMARK 465 LYS B 303 REMARK 465 LYS B 304 REMARK 465 TRP B 305 REMARK 465 LYS B 306 REMARK 465 GLN B 307 REMARK 465 SER B 308 REMARK 465 VAL B 309 REMARK 465 ARG B 310 REMARK 465 LEU B 311 REMARK 465 ILE B 312 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 SER A 51 OG REMARK 470 SER A 52 OG REMARK 470 ARG A 53 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 GLU A 235 CG CD OE1 OE2 REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 SER A 308 OG REMARK 470 VAL A 309 CG1 CG2 REMARK 470 ARG A 310 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 6 CG CD OE1 NE2 REMARK 470 GLN B 23 CG CD OE1 NE2 REMARK 470 PHE B 24 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 ARG B 53 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 58 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 86 CG CD CE NZ REMARK 470 GLU B 109 CG CD OE1 OE2 REMARK 470 GLU B 115 CG CD OE1 OE2 REMARK 470 GLU B 118 CG CD OE1 OE2 REMARK 470 GLU B 143 CG CD OE1 OE2 REMARK 470 ARG B 150 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 154 CG CD CE NZ REMARK 470 GLU B 235 CG CD OE1 OE2 REMARK 470 GLU B 237 CG CD OE1 OE2 REMARK 470 ASP B 238 CG OD1 OD2 REMARK 470 LYS B 262 CG CD CE NZ REMARK 470 LYS B 276 CG CD CE NZ REMARK 470 LYS B 278 CG CD CE NZ REMARK 470 LEU B 284 CG CD1 CD2 REMARK 470 LYS B 287 CG CD CE NZ REMARK 470 LYS B 295 CG CD CE NZ REMARK 470 LYS B 297 CG CD CE NZ REMARK 470 LYS B 298 CG CD CE NZ REMARK 470 ARG B 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 ASP A 161 O HOH A 2107 1.75 REMARK 500 NH1 ARG A 63 O HOH A 2034 1.99 REMARK 500 O HOH A 2002 O HOH A 2004 2.14 REMARK 500 O HOH B 2045 O HOH B 2060 2.16 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 PHE A 162 CZ PHE A 162 CE2 0.118 REMARK 500 GLU A 182 CB GLU A 182 CG -0.114 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 53 -2.01 -57.19 REMARK 500 ASN A 85 -165.87 -124.07 REMARK 500 ASN A 151 58.69 -95.35 REMARK 500 ASP A 161 79.81 62.74 REMARK 500 ASP A 161 75.02 68.08 REMARK 500 ASN B 85 -164.26 -121.75 REMARK 500 ASP B 139 32.85 -150.36 REMARK 500 ASN B 151 53.55 -104.85 REMARK 500 ASP B 161 81.19 62.57 REMARK 500 ASP B 161 82.29 61.26 REMARK 500 REMARK 500 REMARK: NULL 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 A1313 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 144 OD1 REMARK 620 2 ASP A 161 OD2 98.0 REMARK 620 3 ASP A 161 OD2 93.4 64.2 REMARK 620 4 HOH A2095 O 97.2 94.6 157.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 144 OD1 REMARK 620 2 ASP B 161 OD2 69.1 REMARK 620 3 ASP B 161 OD2 105.5 68.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1303 REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 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: 2XUU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DAP-KINASE 1 MUTANT 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: 2Y4P RELATED DB: PDB REMARK 900 DIMERIC STRUCTURE OF DAPK-1 CATALYTIC DOMAIN DBREF 2XZS A 2 312 UNP P53355 DAPK1_HUMAN 2 312 DBREF 2XZS B 2 312 UNP P53355 DAPK1_HUMAN 2 312 SEQADV 2XZS GLY A 1 UNP P53355 EXPRESSION TAG SEQADV 2XZS GLY B 1 UNP P53355 EXPRESSION TAG SEQRES 1 A 312 GLY THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 A 312 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 A 312 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 A 312 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 A 312 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 A 312 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 A 312 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 A 312 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 A 312 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 A 312 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 A 312 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 A 312 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 A 312 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 A 312 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO GLU SEQRES 15 A 312 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 A 312 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 A 312 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 A 312 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 A 312 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 A 312 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 A 312 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 A 312 TRP ILE LYS PRO LYS ASP THR GLN GLN ALA LEU SER ARG SEQRES 23 A 312 LYS ALA SER ALA VAL ASN MET GLU LYS PHE LYS LYS PHE SEQRES 24 A 312 ALA ALA ARG LYS LYS TRP LYS GLN SER VAL ARG LEU ILE SEQRES 1 B 312 GLY THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 B 312 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 B 312 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 B 312 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 B 312 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 B 312 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 B 312 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 B 312 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 B 312 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 B 312 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 B 312 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 B 312 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 B 312 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 B 312 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO GLU SEQRES 15 B 312 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 B 312 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 B 312 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 B 312 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 B 312 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 B 312 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 B 312 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 B 312 TRP ILE LYS PRO LYS ASP THR GLN GLN ALA LEU SER ARG SEQRES 23 B 312 LYS ALA SER ALA VAL ASN MET GLU LYS PHE LYS LYS PHE SEQRES 24 B 312 ALA ALA ARG LYS LYS TRP LYS GLN SER VAL ARG LEU ILE HET MG A1313 1 HET MG B1303 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *243(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 GLU A 107 1 8 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 VAL A 232 1 12 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 HELIX 16 16 ASN B 8 ASP B 11 5 4 HELIX 17 17 SER B 57 ILE B 71 1 15 HELIX 18 18 GLU B 100 GLU B 107 1 8 HELIX 19 19 THR B 112 LEU B 133 1 22 HELIX 20 20 LYS B 141 GLU B 143 5 3 HELIX 21 21 THR B 180 VAL B 184 5 5 HELIX 22 22 ALA B 185 ASN B 190 1 6 HELIX 23 23 LEU B 196 GLY B 213 1 18 HELIX 24 24 THR B 221 ALA B 231 1 11 HELIX 25 25 GLU B 237 SER B 242 1 6 HELIX 26 26 SER B 245 LEU B 256 1 12 HELIX 27 27 ASP B 259 ARG B 263 5 5 HELIX 28 28 THR B 265 HIS B 272 1 8 HELIX 29 29 ASP B 279 SER B 289 1 11 HELIX 30 30 ASN B 292 ALA B 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 SHEET 1 BA 5 TYR B 13 GLY B 22 0 SHEET 2 BA 5 ALA B 25 GLU B 32 -1 O ALA B 25 N GLY B 22 SHEET 3 BA 5 GLN B 38 LYS B 45 -1 O TYR B 39 N CYS B 30 SHEET 4 BA 5 ASP B 88 GLU B 94 -1 O VAL B 89 N ILE B 44 SHEET 5 BA 5 LEU B 79 GLU B 84 -1 N HIS B 80 O ILE B 92 SHEET 1 BB 2 ILE B 135 ALA B 136 0 SHEET 2 BB 2 HIS B 166 LYS B 167 -1 O HIS B 166 N ALA B 136 SHEET 1 BC 2 ILE B 145 LEU B 147 0 SHEET 2 BC 2 ILE B 157 ILE B 159 -1 O LYS B 158 N MET B 146 LINK OD1 ASN A 144 MG MG A1313 1555 1555 2.08 LINK OD2BASP A 161 MG MG A1313 1555 1555 2.45 LINK OD2AASP A 161 MG MG A1313 1555 1555 2.05 LINK MG MG A1313 O HOH A2095 1555 1555 2.07 LINK OD1 ASN B 144 MG MG B1303 1555 1555 2.60 LINK OD2AASP B 161 MG MG B1303 1555 1555 2.42 LINK OD2BASP B 161 MG MG B1303 1555 1555 2.38 SITE 1 AC1 3 ASN A 144 ASP A 161 HOH A2095 SITE 1 AC2 2 ASN B 144 ASP B 161 CRYST1 56.300 49.610 130.500 90.00 94.52 90.00 P 1 21 1 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 0.017762 0.000000 0.001404 0.00000 SCALE2 0.000000 0.020157 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007687 0.00000 MTRIX1 1 -0.997360 -0.068390 0.024450 -5.20665 1 MTRIX2 1 -0.069540 0.802190 -0.593010 17.58542 1 MTRIX3 1 0.020940 -0.593140 -0.804830 54.34247 1