HEADER TRANSFERASE 25-AUG-06 2DXD TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE IN COMPLEX WITH ATP TITLE 2 ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDK,NDP KINASE,NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII (STRAIN ATCC 700860 / DSM SOURCE 3 12428 / JCM 9974 / NBRC 100139 / OT-3); SOURCE 4 ORGANISM_TAXID: 70601; SOURCE 5 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 6 GENE: NDK, PH0698; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS NUCLEOSIDE BINDING, KINASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO-MURAYAMA,K.MURAYAMA,T.TERADA,M.SHIROUZU,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 25-OCT-23 2DXD 1 COMPND REMARK HET HETNAM REVDAT 5 2 1 FORMUL ATOM REVDAT 4 28-APR-21 2DXD 1 COMPND SOURCE REMARK SEQADV REVDAT 3 13-JUL-11 2DXD 1 VERSN REVDAT 2 24-FEB-09 2DXD 1 VERSN REVDAT 1 25-FEB-07 2DXD 0 JRNL AUTH M.KATO-MURAYAMA,K.MURAYAMA,T.TERADA,M.SHIROUZU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE IN JRNL TITL 2 COMPLEX WITH ATP ANALOG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3225959.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 48555 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 SET) : 0.169 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4896 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5190 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 582 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 434 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.14000 REMARK 3 B22 (A**2) : -1.14000 REMARK 3 B33 (A**2) : 2.29000 REMARK 3 B12 (A**2) : 0.10000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.06 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 40.88 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : AMP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : AMP.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000025960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFORCAL MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 87.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 34.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31700 REMARK 200 FOR SHELL : NULL 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 2CWK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA CITRATE, BICINE, 10MM ANP, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 57.81100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.37720 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 64.72367 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 57.81100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 33.37720 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 64.72367 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 57.81100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 33.37720 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 64.72367 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 57.81100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 33.37720 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 64.72367 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 57.81100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 33.37720 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 64.72367 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 57.81100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 33.37720 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 64.72367 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.75439 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 129.44733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 66.75439 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 129.44733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 66.75439 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 129.44733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 66.75439 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 129.44733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 66.75439 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 129.44733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 66.75439 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 129.44733 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 23890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -208.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 51040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 65270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -406.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 PHE A 2 REMARK 465 GLN A 3 REMARK 465 MET A 4 REMARK 465 GLY A 159 REMARK 465 ILE A 160 REMARK 465 MET B 1 REMARK 465 PHE B 2 REMARK 465 GLN B 3 REMARK 465 MET B 4 REMARK 465 GLY B 159 REMARK 465 ILE B 160 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 MET A 41 142.72 -172.55 REMARK 500 LEU A 113 -61.16 -172.51 REMARK 500 SER A 116 -138.97 -110.89 REMARK 500 VAL A 122 -56.67 65.41 REMARK 500 LEU B 113 -60.30 -172.49 REMARK 500 SER B 116 -140.80 -109.41 REMARK 500 VAL B 122 -56.56 64.40 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 B 862 DISTANCE = 6.94 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DXE RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH GDP REMARK 900 RELATED ID: 2DXF RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH GTP ANALOG REMARK 900 RELATED ID: PHO001000698.4 RELATED DB: TARGETDB DBREF 2DXD A 4 160 UNP O58429 NDK_PYRHO 1 157 DBREF 2DXD B 4 160 UNP O58429 NDK_PYRHO 1 157 SEQADV 2DXD MET A 1 UNP O58429 INITIATING METHIONINE SEQADV 2DXD PHE A 2 UNP O58429 EXPRESSION TAG SEQADV 2DXD GLN A 3 UNP O58429 EXPRESSION TAG SEQADV 2DXD MET B 1 UNP O58429 INITIATING METHIONINE SEQADV 2DXD PHE B 2 UNP O58429 EXPRESSION TAG SEQADV 2DXD GLN B 3 UNP O58429 EXPRESSION TAG SEQRES 1 A 160 MET PHE GLN MET SER GLU THR GLU ARG THR LEU VAL ILE SEQRES 2 A 160 ILE LYS PRO ASP ALA VAL VAL ARG GLY LEU ILE GLY GLU SEQRES 3 A 160 ILE ILE SER ARG PHE GLU LYS LYS GLY LEU LYS ILE VAL SEQRES 4 A 160 GLY MET LYS MET ILE TRP ILE ASP ARG GLU LEU ALA GLU SEQRES 5 A 160 LYS HIS TYR GLU GLU HIS ARG GLU LYS PRO PHE PHE LYS SEQRES 6 A 160 ALA LEU ILE ASP TYR ILE THR LYS THR PRO VAL VAL VAL SEQRES 7 A 160 MET VAL LEU GLU GLY ARG TYR ALA VAL GLU VAL VAL ARG SEQRES 8 A 160 LYS MET ALA GLY ALA THR ASP PRO LYS ASP ALA ALA PRO SEQRES 9 A 160 GLY THR ILE ARG GLY ASP PHE GLY LEU GLU VAL SER ASP SEQRES 10 A 160 ALA ILE CYS ASN VAL ILE HIS ALA SER ASP SER LYS GLU SEQRES 11 A 160 SER ALA GLU ARG GLU ILE SER LEU PHE PHE LYS PRO GLU SEQRES 12 A 160 GLU LEU PHE GLU TYR PRO ARG ALA ALA ASP TRP PHE TYR SEQRES 13 A 160 LYS LYS GLY ILE SEQRES 1 B 160 MET PHE GLN MET SER GLU THR GLU ARG THR LEU VAL ILE SEQRES 2 B 160 ILE LYS PRO ASP ALA VAL VAL ARG GLY LEU ILE GLY GLU SEQRES 3 B 160 ILE ILE SER ARG PHE GLU LYS LYS GLY LEU LYS ILE VAL SEQRES 4 B 160 GLY MET LYS MET ILE TRP ILE ASP ARG GLU LEU ALA GLU SEQRES 5 B 160 LYS HIS TYR GLU GLU HIS ARG GLU LYS PRO PHE PHE LYS SEQRES 6 B 160 ALA LEU ILE ASP TYR ILE THR LYS THR PRO VAL VAL VAL SEQRES 7 B 160 MET VAL LEU GLU GLY ARG TYR ALA VAL GLU VAL VAL ARG SEQRES 8 B 160 LYS MET ALA GLY ALA THR ASP PRO LYS ASP ALA ALA PRO SEQRES 9 B 160 GLY THR ILE ARG GLY ASP PHE GLY LEU GLU VAL SER ASP SEQRES 10 B 160 ALA ILE CYS ASN VAL ILE HIS ALA SER ASP SER LYS GLU SEQRES 11 B 160 SER ALA GLU ARG GLU ILE SER LEU PHE PHE LYS PRO GLU SEQRES 12 B 160 GLU LEU PHE GLU TYR PRO ARG ALA ALA ASP TRP PHE TYR SEQRES 13 B 160 LYS LYS GLY ILE HET CL A 701 1 HET AMP A 501 23 HET CL B 702 1 HET AMP B 502 23 HETNAM CL CHLORIDE ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 3 CL 2(CL 1-) FORMUL 4 AMP 2(C10 H14 N5 O7 P) FORMUL 7 HOH *434(H2 O) HELIX 1 1 LYS A 15 ARG A 21 1 7 HELIX 2 2 LEU A 23 GLY A 35 1 13 HELIX 3 3 ASP A 47 TYR A 55 1 9 HELIX 4 4 GLU A 56 ARG A 59 5 4 HELIX 5 5 PHE A 63 THR A 72 1 10 HELIX 6 6 TYR A 85 GLY A 95 1 11 HELIX 7 7 ASP A 98 ALA A 102 5 5 HELIX 8 8 THR A 106 GLY A 112 1 7 HELIX 9 9 SER A 128 PHE A 140 1 13 HELIX 10 10 LYS A 141 LEU A 145 5 5 HELIX 11 11 ALA A 152 LYS A 157 5 6 HELIX 12 12 LYS B 15 ARG B 21 1 7 HELIX 13 13 LEU B 23 GLY B 35 1 13 HELIX 14 14 ASP B 47 TYR B 55 1 9 HELIX 15 15 GLU B 56 ARG B 59 5 4 HELIX 16 16 PHE B 63 THR B 72 1 10 HELIX 17 17 TYR B 85 GLY B 95 1 11 HELIX 18 18 ASP B 98 ALA B 102 5 5 HELIX 19 19 THR B 106 GLY B 112 1 7 HELIX 20 20 SER B 128 PHE B 140 1 13 HELIX 21 21 LYS B 141 LEU B 145 5 5 HELIX 22 22 ALA B 152 LYS B 157 5 6 SHEET 1 A 4 LYS A 37 ILE A 44 0 SHEET 2 A 4 VAL A 76 ARG A 84 -1 O VAL A 76 N ILE A 44 SHEET 3 A 4 THR A 7 ILE A 14 -1 N ILE A 14 O VAL A 77 SHEET 4 A 4 ILE A 123 ALA A 125 -1 O HIS A 124 N ILE A 13 SHEET 1 B 4 LYS B 37 ILE B 44 0 SHEET 2 B 4 VAL B 76 ARG B 84 -1 O VAL B 76 N ILE B 44 SHEET 3 B 4 THR B 7 ILE B 14 -1 N ILE B 14 O VAL B 77 SHEET 4 B 4 ILE B 123 ALA B 125 -1 O HIS B 124 N ILE B 13 SITE 1 AC1 6 GLY A 95 ALA A 96 ALA A 102 ALA A 103 SITE 2 AC1 6 HOH A 877 HOH A 923 SITE 1 AC2 5 GLY B 95 ALA B 96 ALA B 102 ALA B 103 SITE 2 AC2 5 HOH B 884 SITE 1 AC3 9 LYS A 15 HIS A 58 PHE A 63 THR A 97 SITE 2 AC3 9 ILE A 119 ASN A 121 HOH A 763 HOH A 782 SITE 3 AC3 9 HOH A 871 SITE 1 AC4 12 LYS B 15 TYR B 55 HIS B 58 PHE B 63 SITE 2 AC4 12 THR B 97 ARG B 108 ILE B 119 ASN B 121 SITE 3 AC4 12 HOH B 723 HOH B 755 HOH B 790 HOH B 905 CRYST1 115.622 115.622 194.171 90.00 90.00 120.00 H 3 2 36 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 0.008649 0.004993 0.000000 0.00000 SCALE2 0.000000 0.009987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005150 0.00000