10 20 30 40 50 60 70 80 3F5U - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER TRANSFERASE 04-NOV-08 3F5U
TITLE CRYSTAL STRUCTURE OF THE DEATH ASSOCIATED PROTEIN KINASE IN TITLE 2 COMPLEX WITH AMPPNP AND MG2+
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-285, PROTEIN KINASE DOMAIN, COMPND 5 CATALYTIC DOMAIN; COMPND 6 SYNONYM: DAP KINASE 1; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DAPK, DAPK1, DEATH-ASSOCIATED PROTEIN KINASE 1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOP10; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PASK-IBA3
KEYWDS KINASE-AMPPNP COMPLEX, ALTERNATIVE SPLICING, ANK REPEAT, KEYWDS 2 APOPTOSIS, ATP-BINDING, CALMODULIN-BINDING, CYTOPLASM, KEYWDS 3 KINASE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 4 SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR L.K.MCNAMARA,D.M.WATTERSON,J.S.BRUNZELLE
REVDAT 1 24-MAR-09 3F5U 0
JRNL AUTH L.K.MCNAMARA,D.M.WATTERSON,J.S.BRUNZELLE JRNL TITL STRUCTURAL INSIGHT INTO NUCLEOTIDE RECOGNITION BY JRNL TITL 2 HUMAN DEATH-ASSOCIATED PROTEIN KINASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 241 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19237746 JRNL DOI 10.1107/S0907444908043679
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 17521 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 941 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) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1127 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2453 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : -0.97000 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): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.189 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2552 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3483 ; 1.773 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 316 ; 6.717 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;38.803 ;24.880 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 463 ;17.429 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;22.440 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 380 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1965 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1180 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1763 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 135 ; 0.155 ; 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): 95 ; 0.258 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.345 ; 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): 1562 ; 1.156 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2492 ; 1.831 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1116 ; 2.834 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 991 ; 4.287 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3F5U COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-08. REMARK 100 THE RCSB ID CODE IS RCSB050183.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : SINGLE DIAMOND CRYSTAL REMARK 200 OPTICS : BE LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18512 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 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: PDB ENTRY 1JKS REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 2.2 M AMMONIUM SULFATE REMARK 280 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
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 23.33450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.29950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.23050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.29950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.33450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.23050 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 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 278 REMARK 465 ASP A 279 REMARK 465 THR A 280 REMARK 465 GLN A 281 REMARK 465 GLN A 282 REMARK 465 ALA A 283 REMARK 465 LEU A 284 REMARK 465 SER A 285 REMARK 465 SER A 286 REMARK 465 ALA A 287 REMARK 465 TRP A 288 REMARK 465 SER A 289 REMARK 465 HIS A 290 REMARK 465 LYS A 295
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 107 CA C O CB CG CD OE1 REMARK 480 GLU A 107 OE2 REMARK 480 ARG A 156 NE CZ NH1 NH2
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 OE1 GLN A 223 O HOH A 354 3545 1.42 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 GLU A 109 N - CA - C ANGL. DEV. = 16.5 DEGREES REMARK 500 LYS A 108 CA - C - N ANGL. DEV. = -26.0 DEGREES REMARK 500 ASN A 176 N - CA - C ANGL. DEV. = 22.9 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 PHE A 24 -20.45 85.77 REMARK 500 GLN A 72 94.63 -161.11 REMARK 500 ASP A 139 37.59 -144.40 REMARK 500 ASP A 161 76.98 63.10 REMARK 500 ASN A 176 49.40 71.42 REMARK 500 PHE A 178 115.62 -161.85 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 GLU A 107 LYS A 108 102.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 107 12.21 REMARK 500 LYS A 108 -26.43 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 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: (11X,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 A 109 7.2 L D EXPECTING SP3 REMARK 500 ASN A 176 14.7 L L OUTSIDE RANGE REMARK 500 ILE A 177 45.8 L L OUTSIDE RANGE 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 A 297 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 161 OD2 REMARK 620 2 ANP A 296 O2G 75.0 REMARK 620 3 ANP A 296 O3G 134.0 67.0 REMARK 620 4 ANP A 296 O1A 103.7 153.2 99.2 REMARK 620 5 HOH A 397 O 128.7 125.3 95.0 76.9 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 296 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 297 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 298
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F5G RELATED DB: PDB REMARK 900 DAPK-ADP-MG2+ REMARK 900 RELATED ID: 1JKS RELATED DB: PDB REMARK 900 DAPK-APO REMARK 900 RELATED ID: 1JKK RELATED DB: PDB REMARK 900 DAPK-AMPPPNP-MG REMARK 900 RELATED ID: 1IG1 RELATED DB: PDB REMARK 900 DAPK-AMPPNP-MN
DBREF 3F5U A 1 285 UNP P53355 DAPK1_HUMAN 1 285
SEQADV 3F5U SER A 286 UNP P53355 EXPRESSION TAG SEQADV 3F5U ALA A 287 UNP P53355 EXPRESSION TAG SEQADV 3F5U TRP A 288 UNP P53355 EXPRESSION TAG SEQADV 3F5U SER A 289 UNP P53355 EXPRESSION TAG SEQADV 3F5U HIS A 290 UNP P53355 EXPRESSION TAG SEQADV 3F5U PRO A 291 UNP P53355 EXPRESSION TAG SEQADV 3F5U GLN A 292 UNP P53355 EXPRESSION TAG SEQADV 3F5U PHE A 293 UNP P53355 EXPRESSION TAG SEQADV 3F5U GLU A 294 UNP P53355 EXPRESSION TAG SEQADV 3F5U LYS A 295 UNP P53355 EXPRESSION TAG
SEQRES 1 A 295 MET THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 A 295 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 A 295 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 A 295 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 A 295 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 A 295 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 A 295 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 A 295 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 A 295 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 A 295 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 A 295 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 A 295 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 A 295 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 A 295 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO GLU SEQRES 15 A 295 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 A 295 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 A 295 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 A 295 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 A 295 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 A 295 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 A 295 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 A 295 TRP ILE LYS PRO LYS ASP THR GLN GLN ALA LEU SER SER SEQRES 23 A 295 ALA TRP SER HIS PRO GLN PHE GLU LYS
HET ANP A 296 31 HET MG A 297 1 HET SO4 A 298 5
HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION
FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *99(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 THR A 265 HIS A 272 1 8
SHEET 1 A 5 TYR A 13 SER A 21 0 SHEET 2 A 5 ALA A 25 GLU A 32 -1 O LYS A 29 N GLY A 16 SHEET 3 A 5 GLN A 38 LYS A 45 -1 O ALA A 41 N LYS A 28 SHEET 4 A 5 ASP A 88 GLU A 94 -1 O VAL A 89 N ILE A 44 SHEET 5 A 5 LEU A 79 GLU A 84 -1 N TYR A 83 O ILE 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 ILE A 159 -1 O LYS A 158 N MET A 146
LINK OD2 ASP A 161 MG MG A 297 1555 1555 2.11 LINK O2G ANP A 296 MG MG A 297 1555 1555 2.49 LINK O3G ANP A 296 MG MG A 297 1555 1555 2.14 LINK O1A ANP A 296 MG MG A 297 1555 1555 2.08 LINK MG MG A 297 O HOH A 397 1555 1555 2.24
SITE 1 AC1 19 LEU A 19 GLY A 20 SER A 21 GLY A 22 SITE 2 AC1 19 GLN A 23 VAL A 27 ALA A 40 LYS A 42 SITE 3 AC1 19 ILE A 77 GLU A 94 VAL A 96 GLU A 100 SITE 4 AC1 19 ASP A 139 ILE A 160 ASP A 161 MG A 297 SITE 5 AC1 19 HOH A 325 HOH A 397 HOH A 398 SITE 1 AC2 4 ASN A 144 ASP A 161 ANP A 296 HOH A 397 SITE 1 AC3 3 ARG A 63 LYS A 175 HOH A 310
CRYST1 46.669 62.461 88.599 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 0.021428 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016010 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011287 0.00000