PDB Short entry for 2W4J HEADER TRANSFERASE 27-NOV-08 2W4J TITLE X-RAY STRUCTURE OF A DAP-KINASE 2-277 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 1-277; COMPND 5 SYNONYM: DEATH ASSOCIATED PROTEIN KINASE I DAPK, 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: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS POLYMORPHISM, PHOSPHOPROTEIN, CALMODULIN-BINDING, SERINE/THREONINE- KEYWDS 2 PROTEIN KINASE, NUCLEOTIDE-BINDING, ALTERNATIVE SPLICING, DAPK, KEYWDS 3 KINASE, COMPLEX, APOPTOSIS, CYTOPLASM, ANK REPEAT, CALMODULIN, KEYWDS 4 TRANSFERASE, ATP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR I.DE DIEGO,J.KUPER,F.LEHMANN,M.WILMANNS REVDAT 3 13-DEC-23 2W4J 1 REMARK LINK REVDAT 2 24-JUL-19 2W4J 1 REMARK REVDAT 1 22-DEC-09 2W4J 0 JRNL AUTH I.DE DIEGO,J.KUPER,F.LEHMANN,M.WILMANNS JRNL TITL X-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0044 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 61052 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3257 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4338 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 249 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2228 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.25000 REMARK 3 B22 (A**2) : 0.53000 REMARK 3 B33 (A**2) : 0.73000 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): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.379 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2384 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1628 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3249 ; 1.874 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4002 ; 1.024 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 6.223 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.686 ;24.870 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 435 ;14.173 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.880 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2631 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 0.001 ; 0.020 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): 1417 ; 2.004 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2314 ; 2.928 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 967 ; 3.924 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 922 ; 5.652 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2W4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290038203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90497 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 64311 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 62.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1JKS REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 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 23.42200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.17250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.16800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.17250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.42200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.16800 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: PQS 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 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 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 GLU A 109 CG CD OE1 OE2 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 O HOH A 2297 O HOH A 2309 1.93 REMARK 500 O HOH A 2062 O HOH A 2305 1.99 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 2123 O HOH A 2137 2665 1.86 REMARK 500 O HOH A 2076 O HOH A 2298 2664 2.03 REMARK 500 O HOH A 2122 O HOH A 2140 2665 2.14 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 GLU A 113 CD GLU A 113 OE2 -0.073 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 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 253 NE - CZ - NH1 ANGL. DEV. = -4.8 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 110 136.02 -39.17 REMARK 500 ASP A 139 37.83 -150.74 REMARK 500 ASN A 151 45.43 -108.58 REMARK 500 ASP A 161 81.91 63.17 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 A2015 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A2116 DISTANCE = 6.50 ANGSTROMS 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 A1280 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 144 OD1 REMARK 620 2 ASP A 161 OD2 87.4 REMARK 620 3 ADP A1278 O2B 176.0 88.9 REMARK 620 4 ADP A1278 O2A 92.9 90.1 85.5 REMARK 620 5 HOH A2199 O 91.0 87.7 90.5 175.4 REMARK 620 6 HOH A2350 O 87.8 175.1 95.9 91.0 91.5 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 1278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1279 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1280 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: 1P4F RELATED DB: PDB REMARK 900 DEATH ASSOCIATED PROTEIN KINASE CATALYTIC DOMAIN WITH REMARK 900 BOUNDINHIBITOR FRAGMENT REMARK 900 RELATED ID: 2X0G RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX REMARK 900 RELATED ID: 2W4K RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A DAP-KINASE 2-302 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: 1JKT RELATED DB: PDB REMARK 900 TETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED REMARK 900 PROTEIN KINASE 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 DBREF 2W4J A 1 277 UNP P53355 DAPK1_HUMAN 1 277 SEQRES 1 A 277 MET THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 A 277 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 A 277 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 A 277 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 A 277 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 A 277 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 A 277 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 A 277 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 A 277 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 A 277 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 A 277 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 A 277 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 A 277 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 A 277 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO GLU SEQRES 15 A 277 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 A 277 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 A 277 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 A 277 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 A 277 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 A 277 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 A 277 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 A 277 TRP ILE LYS PRO HET ADP A1278 27 HET ACT A1279 4 HET MG A1280 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ACT ACETATE ION HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 MG MG 2+ FORMUL 5 HOH *351(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 LYS A 108 1 9 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 ALA A 185 ASN A 190 1 6 HELIX 7 7 LEU A 196 GLY A 213 1 18 HELIX 8 8 THR A 221 ALA A 231 1 11 HELIX 9 9 GLU A 237 SER A 242 1 6 HELIX 10 10 SER A 245 LEU A 256 1 12 HELIX 11 11 ASP A 259 ARG A 263 5 5 HELIX 12 12 THR A 265 HIS A 272 1 8 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 OD1 ASN A 144 MG MG A1280 1555 1555 2.25 LINK OD2 ASP A 161 MG MG A1280 1555 1555 2.13 LINK O2B ADP A1278 MG MG A1280 1555 1555 1.98 LINK O2A ADP A1278 MG MG A1280 1555 1555 2.03 LINK MG MG A1280 O HOH A2199 1555 1555 2.08 LINK MG MG A1280 O HOH A2350 1555 1555 1.96 SITE 1 AC1 24 LEU A 19 GLY A 20 SER A 21 GLY A 22 SITE 2 AC1 24 ALA A 25 VAL A 27 ALA A 40 LYS A 42 SITE 3 AC1 24 GLU A 94 VAL A 96 GLU A 100 GLU A 143 SITE 4 AC1 24 ASN A 144 MET A 146 ILE A 160 ASP A 161 SITE 5 AC1 24 MG A1280 HOH A2030 HOH A2152 HOH A2199 SITE 6 AC1 24 HOH A2346 HOH A2347 HOH A2348 HOH A2350 SITE 1 AC2 7 GLY A 16 LYS A 29 CYS A 30 ARG A 31 SITE 2 AC2 7 GLN A 38 PRO A 193 HOH A2351 SITE 1 AC3 5 ASN A 144 ASP A 161 ADP A1278 HOH A2199 SITE 2 AC3 5 HOH A2350 CRYST1 46.844 62.336 88.345 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 0.021347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011319 0.00000