PDB Short entry for 1YRP HEADER TRANSFERASE 04-FEB-05 1YRP TITLE CATALYTIC DOMAIN OF HUMAN ZIP KINASE PHOSPHORYLATED AT THR265 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: ZIP-KINASE, DAP KINASE 3, DAP- LIKE KINASE, DLK; COMPND 6 EC: 2.7.1.37; 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: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST-15 KEYWDS KINASE FOLD, PHOSPHOTHREONINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.KURSULA,J.VAHOKOSKI,M.WILMANNS REVDAT 4 18-MAY-16 1YRP 1 JRNL REVDAT 3 13-JUL-11 1YRP 1 VERSN REVDAT 2 24-FEB-09 1YRP 1 VERSN REVDAT 1 20-JUN-06 1YRP 0 JRNL AUTH B.SIMON,A.S.HUART,K.TEMMERMAN,J.VAHOKOSKI,H.D.MERTENS, JRNL AUTH 2 D.KOMADINA,J.E.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 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27133022 JRNL DOI 10.1016/J.STR.2016.03.020 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 10171 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 509 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 673 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4490 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 34.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.83000 REMARK 3 B22 (A**2) : 4.69000 REMARK 3 B33 (A**2) : -4.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.582 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.503 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 62.478 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.880 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.849 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4583 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4201 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6176 ; 1.240 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9791 ; 1.259 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 550 ; 6.910 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;35.182 ;24.174 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 854 ;17.408 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;21.794 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 680 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5038 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 936 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 900 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4220 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2134 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2674 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 95 ; 0.103 ; 0.200 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): 23 ; 0.264 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 50 ; 0.266 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.301 ; 0.200 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): 3589 ; 0.101 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1122 ; 0.041 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4446 ; 0.148 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2106 ; 0.210 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1730 ; 0.316 ; 5.000 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 2 A 277 1 REMARK 3 1 B 2 B 277 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 4342 ; .03 ; .05 REMARK 3 TIGHT THERMAL 1 A (A**2): 4342 ; .01 ; .50 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 2 A 277 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5592 .0822 28.6464 REMARK 3 T TENSOR REMARK 3 T11: -.1465 T22: -.1889 REMARK 3 T33: -.2020 T12: .0375 REMARK 3 T13: .0393 T23: -.0046 REMARK 3 L TENSOR REMARK 3 L11: 4.3337 L22: 1.4481 REMARK 3 L33: 1.0084 L12: 1.2200 REMARK 3 L13: .9626 L23: -.2832 REMARK 3 S TENSOR REMARK 3 S11: .0911 S12: -.2185 S13: -.0158 REMARK 3 S21: .0757 S22: -.0916 S23: .1665 REMARK 3 S31: .0762 S32: -.1130 S33: .0006 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 2 B 277 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3248 24.4886 12.1161 REMARK 3 T TENSOR REMARK 3 T11: -.1581 T22: -.1555 REMARK 3 T33: -.1046 T12: -.0178 REMARK 3 T13: -.0044 T23: .0649 REMARK 3 L TENSOR REMARK 3 L11: 1.2955 L22: 1.6519 REMARK 3 L33: 3.9118 L12: -.7735 REMARK 3 L13: -.4050 L23: 1.2479 REMARK 3 S TENSOR REMARK 3 S11: -.0252 S12: -.1657 S13: .0693 REMARK 3 S21: .0580 S22: -.0997 S23: .1506 REMARK 3 S31: -.0952 S32: -.4070 S33: .1249 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 1YRP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-05. REMARK 100 THE RCSB ID CODE IS RCSB031853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-04 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) : NULL 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10171 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, MGCL2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K 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 30.46500 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: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 0 REMARK 465 MET A 1 REMARK 465 GLY B 0 REMARK 465 MET B 1 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 CD - NE - CZ ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = -9.3 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 58 CD - NE - CZ ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 63 CD - NE - CZ ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG A 254 CD - NE - CZ ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 254 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 254 NE - CZ - NH2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 262 CD - NE - CZ ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 262 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 262 NE - CZ - NH2 ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG A 263 CD - NE - CZ ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG A 263 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 263 NE - CZ - NH2 ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG B 47 CD - NE - CZ ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG B 47 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG B 47 NE - CZ - NH2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG B 58 CD - NE - CZ ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG B 58 NE - CZ - NH1 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG B 58 NE - CZ - NH2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG B 63 CD - NE - CZ ANGL. DEV. = 11.3 DEGREES REMARK 500 ARG B 63 NE - CZ - NH1 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG B 63 NE - CZ - NH2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG B 254 CD - NE - CZ ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG B 254 NE - CZ - NH1 ANGL. DEV. = -9.3 DEGREES REMARK 500 ARG B 254 NE - CZ - NH2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG B 262 CD - NE - CZ ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG B 262 NE - CZ - NH1 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG B 262 NE - CZ - NH2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG B 263 CD - NE - CZ ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG B 263 NE - CZ - NH1 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG B 263 NE - CZ - NH2 ANGL. DEV. = 7.5 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 GLU A 17 112.05 -14.39 REMARK 500 LEU A 19 -96.87 -103.93 REMARK 500 GLN A 23 -70.33 -60.18 REMARK 500 ARG A 48 -144.54 -76.40 REMARK 500 SER A 50 -72.87 -11.91 REMARK 500 ARG A 72 91.24 -163.60 REMARK 500 ASN A 75 34.46 -93.32 REMARK 500 PHE A 138 -4.00 71.02 REMARK 500 ASP A 161 101.36 67.46 REMARK 500 ASN A 172 -169.93 -118.03 REMARK 500 ASN A 176 171.85 175.90 REMARK 500 GLU A 238 -39.04 -39.12 REMARK 500 GLU B 17 112.27 -14.35 REMARK 500 LEU B 19 -96.41 -104.18 REMARK 500 GLN B 23 -71.11 -59.81 REMARK 500 ARG B 48 -144.91 -77.10 REMARK 500 SER B 50 -72.96 -11.38 REMARK 500 ARG B 72 90.96 -164.07 REMARK 500 ASN B 75 34.87 -92.91 REMARK 500 GLU B 109 -26.75 -22.07 REMARK 500 PHE B 138 -3.89 70.82 REMARK 500 ASP B 161 101.54 67.06 REMARK 500 ASN B 176 170.76 175.28 REMARK 500 GLU B 238 -39.62 -38.53 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 108 GLU A 109 -72.51 REMARK 500 ALA A 170 GLY A 171 145.42 REMARK 500 LYS B 108 GLU B 109 -112.31 REMARK 500 ALA B 170 GLY B 171 146.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 58 0.08 SIDE CHAIN REMARK 500 ARG A 63 0.10 SIDE CHAIN REMARK 500 ARG A 254 0.11 SIDE CHAIN REMARK 500 ARG A 262 0.10 SIDE CHAIN REMARK 500 ARG A 263 0.11 SIDE CHAIN REMARK 500 ARG B 47 0.09 SIDE CHAIN REMARK 500 ARG B 58 0.08 SIDE CHAIN REMARK 500 ARG B 254 0.07 SIDE CHAIN REMARK 500 ARG B 262 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU B 109 24.6 L L OUTSIDE RANGE 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 RESIDUE DTT B 278 DBREF 1YRP A 1 277 UNP O43293 DAPK3_HUMAN 1 277 DBREF 1YRP B 1 277 UNP O43293 DAPK3_HUMAN 1 277 SEQADV 1YRP GLY A 0 UNP O43293 EXPRESSION TAG SEQADV 1YRP GLY B 0 UNP O43293 EXPRESSION TAG SEQRES 1 A 278 GLY MET SER THR PHE ARG GLN GLU ASP VAL GLU ASP HIS SEQRES 2 A 278 TYR GLU MET GLY GLU GLU LEU GLY SER GLY GLN PHE ALA SEQRES 3 A 278 ILE VAL ARG LYS CYS ARG GLN LYS GLY THR GLY LYS GLU SEQRES 4 A 278 TYR ALA ALA LYS PHE ILE LYS LYS ARG ARG LEU SER SER SEQRES 5 A 278 SER ARG ARG GLY VAL SER ARG GLU GLU ILE GLU ARG GLU SEQRES 6 A 278 VAL ASN ILE LEU ARG GLU ILE ARG HIS PRO ASN ILE ILE SEQRES 7 A 278 THR LEU HIS ASP ILE PHE GLU ASN LYS THR ASP VAL VAL SEQRES 8 A 278 LEU ILE LEU GLU LEU VAL SER GLY GLY GLU LEU PHE ASP SEQRES 9 A 278 PHE LEU ALA GLU LYS GLU SER LEU THR GLU ASP GLU ALA SEQRES 10 A 278 THR GLN PHE LEU LYS GLN ILE LEU ASP GLY VAL HIS TYR SEQRES 11 A 278 LEU HIS SER LYS ARG ILE ALA HIS PHE ASP LEU LYS PRO SEQRES 12 A 278 GLU ASN ILE MET LEU LEU ASP LYS ASN VAL PRO ASN PRO SEQRES 13 A 278 ARG ILE LYS LEU ILE ASP PHE GLY ILE ALA HIS LYS ILE SEQRES 14 A 278 GLU ALA GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO SEQRES 15 A 278 GLU PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU SEQRES 16 A 278 GLY LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR SEQRES 17 A 278 TYR ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY GLU SEQRES 18 A 278 THR LYS GLN GLU THR LEU THR ASN ILE SER ALA VAL ASN SEQRES 19 A 278 TYR ASP PHE ASP GLU GLU TYR PHE SER ASN THR SER GLU SEQRES 20 A 278 LEU ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP SEQRES 21 A 278 PRO LYS ARG ARG MET TPO ILE ALA GLN SER LEU GLU HIS SEQRES 22 A 278 SER TRP ILE LYS ALA SEQRES 1 B 278 GLY MET SER THR PHE ARG GLN GLU ASP VAL GLU ASP HIS SEQRES 2 B 278 TYR GLU MET GLY GLU GLU LEU GLY SER GLY GLN PHE ALA SEQRES 3 B 278 ILE VAL ARG LYS CYS ARG GLN LYS GLY THR GLY LYS GLU SEQRES 4 B 278 TYR ALA ALA LYS PHE ILE LYS LYS ARG ARG LEU SER SER SEQRES 5 B 278 SER ARG ARG GLY VAL SER ARG GLU GLU ILE GLU ARG GLU SEQRES 6 B 278 VAL ASN ILE LEU ARG GLU ILE ARG HIS PRO ASN ILE ILE SEQRES 7 B 278 THR LEU HIS ASP ILE PHE GLU ASN LYS THR ASP VAL VAL SEQRES 8 B 278 LEU ILE LEU GLU LEU VAL SER GLY GLY GLU LEU PHE ASP SEQRES 9 B 278 PHE LEU ALA GLU LYS GLU SER LEU THR GLU ASP GLU ALA SEQRES 10 B 278 THR GLN PHE LEU LYS GLN ILE LEU ASP GLY VAL HIS TYR SEQRES 11 B 278 LEU HIS SER LYS ARG ILE ALA HIS PHE ASP LEU LYS PRO SEQRES 12 B 278 GLU ASN ILE MET LEU LEU ASP LYS ASN VAL PRO ASN PRO SEQRES 13 B 278 ARG ILE LYS LEU ILE ASP PHE GLY ILE ALA HIS LYS ILE SEQRES 14 B 278 GLU ALA GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO SEQRES 15 B 278 GLU PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU SEQRES 16 B 278 GLY LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR SEQRES 17 B 278 TYR ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY GLU SEQRES 18 B 278 THR LYS GLN GLU THR LEU THR ASN ILE SER ALA VAL ASN SEQRES 19 B 278 TYR ASP PHE ASP GLU GLU TYR PHE SER ASN THR SER GLU SEQRES 20 B 278 LEU ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP SEQRES 21 B 278 PRO LYS ARG ARG MET TPO ILE ALA GLN SER LEU GLU HIS SEQRES 22 B 278 SER TRP ILE LYS ALA MODRES 1YRP TPO A 265 THR PHOSPHOTHREONINE MODRES 1YRP TPO B 265 THR PHOSPHOTHREONINE HET TPO A 265 11 HET TPO B 265 11 HET DTT B 278 8 HETNAM TPO PHOSPHOTHREONINE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN TPO PHOSPHONOTHREONINE HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 1 TPO 2(C4 H10 N O6 P) FORMUL 3 DTT C4 H10 O2 S2 HELIX 1 1 ASP 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 LYS A 133 1 22 HELIX 5 5 ALA A 185 ASN A 190 1 6 HELIX 6 6 LEU A 196 GLY A 213 1 18 HELIX 7 7 THR A 221 VAL A 232 1 12 HELIX 8 8 ASP A 237 SER A 242 1 6 HELIX 9 9 SER A 245 ARG A 254 1 10 HELIX 10 10 TPO A 265 GLU A 271 1 7 HELIX 11 11 ASP B 8 ASP B 11 5 4 HELIX 12 12 SER B 57 ILE B 71 1 15 HELIX 13 13 GLU B 100 GLU B 107 1 8 HELIX 14 14 THR B 112 LYS B 133 1 22 HELIX 15 15 ALA B 185 ASN B 190 1 6 HELIX 16 16 LEU B 196 GLY B 213 1 18 HELIX 17 17 THR B 221 VAL B 232 1 12 HELIX 18 18 ASP B 237 SER B 242 1 6 HELIX 19 19 SER B 245 ARG B 254 1 10 HELIX 20 20 TPO B 265 GLU B 271 1 7 SHEET 1 A 5 TYR A 13 SER A 21 0 SHEET 2 A 5 ALA A 25 GLN A 32 -1 O LYS A 29 N GLU A 17 SHEET 3 A 5 GLU A 38 LYS A 45 -1 O PHE A 43 N ILE A 26 SHEET 4 A 5 ASP A 88 LEU A 93 -1 O LEU A 93 N ALA A 40 SHEET 5 A 5 LEU A 79 GLU A 84 -1 N PHE A 83 O VAL A 90 SHEET 1 B 2 ILE A 135 ALA A 136 0 SHEET 2 B 2 HIS A 166 LYS A 167 -1 O HIS A 166 N ALA A 136 SHEET 1 C 2 ILE A 145 LEU A 147 0 SHEET 2 C 2 ILE A 157 LEU A 159 -1 O LYS A 158 N MET A 146 SHEET 1 D 5 TYR B 13 SER B 21 0 SHEET 2 D 5 ALA B 25 GLN B 32 -1 O LYS B 29 N GLU B 17 SHEET 3 D 5 GLU B 38 LYS B 45 -1 O PHE B 43 N ILE B 26 SHEET 4 D 5 ASP B 88 LEU B 93 -1 O LEU B 93 N ALA B 40 SHEET 5 D 5 LEU B 79 GLU B 84 -1 N PHE B 83 O VAL B 90 SHEET 1 E 2 ILE B 135 ALA B 136 0 SHEET 2 E 2 HIS B 166 LYS B 167 -1 O HIS B 166 N ALA B 136 SHEET 1 F 2 ILE B 145 LEU B 147 0 SHEET 2 F 2 ILE B 157 LEU B 159 -1 O LYS B 158 N MET B 146 LINK C MET A 264 N TPO A 265 1555 1555 1.33 LINK C TPO A 265 N ILE A 266 1555 1555 1.33 LINK C MET B 264 N TPO B 265 1555 1555 1.33 LINK C TPO B 265 N ILE B 266 1555 1555 1.33 SITE 1 AC1 1 ILE B 177 CRYST1 53.560 60.930 87.950 90.00 92.17 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 0.018671 0.000000 0.000706 0.00000 SCALE2 0.000000 0.016412 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011378 0.00000