HEADER PHOSPHOTRANSFERASE 26-MAY-98 2BEF TITLE CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ADP, BEF3, MG++ SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_TAXID: 44689; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRANSFERASE, NUCLEOSIDE DIPHOSPHATE KINASE, PHOSPHORYL KEYWDS 2 TRANSFER, BERYLLIUM FLUORIDE EXPDTA X-RAY DIFFRACTION AUTHOR Y.W.XU,J.CHERFILS REVDAT 5 16-OCT-24 2BEF 1 REMARK REVDAT 4 05-JUN-24 2BEF 1 REMARK LINK REVDAT 3 13-JUL-11 2BEF 1 VERSN REVDAT 2 24-FEB-09 2BEF 1 VERSN REVDAT 1 12-AUG-98 2BEF 0 JRNL AUTH Y.W.XU,S.MORERA,J.JANIN,J.CHERFILS JRNL TITL ALF3 MIMICS THE TRANSITION STATE OF PROTEIN PHOSPHORYLATION JRNL TITL 2 IN THE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE JRNL TITL 3 AND MGADP. JRNL REF PROC.NATL.ACAD.SCI.USA V. 94 3579 1997 JRNL REFN ISSN 0027-8424 JRNL PMID 9108019 JRNL DOI 10.1073/PNAS.94.8.3579 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 20540 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3441 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 4.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.050 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.880 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-96 REMARK 200 TEMPERATURE (KELVIN) : 277 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20554 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.20700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: 100% IDENTITY REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP, SEEDING, 32% PEG550, REMARK 280 50MM TRIS PH 7.5, 20MM MGCL2, 25MM NAF, 1MM BECL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 51.25000 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 102.50000 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 102.50000 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 51.25000 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 300 REMARK: THE DICTYOSTELIUM NDP KINASE HEXAMER IS RECONSTITUTED FROM REMARK 300 THE TRIMER IN THE ASYMMETRIC UNIT FROM CRYSTALLOGRAPHIC REMARK 300 SYMMETRIES. THE POSITION OF BE++ WAS MODELLED IN REMARK 300 TETRAHEDRAL CONFORMATION FROM THE ELECTRON DENSITY OF THE REMARK 300 3 FLUORINE ATOMS. 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: 20620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 102.50000 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 SER A 2 REMARK 465 THR A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 5 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 ASN B 4 REMARK 465 LYS B 5 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 THR C 3 REMARK 465 ASN C 4 REMARK 465 LYS C 5 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 VAL A 114 -19.37 -140.94 REMARK 500 ILE A 120 -39.86 62.88 REMARK 500 PRO A 151 5.37 -65.67 REMARK 500 ASN B 7 25.49 -76.64 REMARK 500 ILE B 120 -49.48 56.11 REMARK 500 PRO B 149 -128.07 -85.32 REMARK 500 TYR C 56 37.87 -94.31 REMARK 500 ARG C 118 64.02 -117.27 REMARK 500 ILE C 120 -45.23 63.34 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 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BEF A 157 F3 REMARK 620 2 ADP A 158 O1B 94.8 REMARK 620 3 ADP A 158 O1A 106.5 83.0 REMARK 620 4 HOH A 619 O 83.7 174.2 92.1 REMARK 620 5 HOH A 626 O 88.1 85.1 161.8 100.4 REMARK 620 6 HOH A 693 O 169.5 82.6 83.3 99.9 81.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A 157 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 158 O3B REMARK 620 2 BEF A 157 F1 94.7 REMARK 620 3 BEF A 157 F2 108.7 109.4 REMARK 620 4 BEF A 157 F3 121.6 108.8 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BEF B 157 F1 REMARK 620 2 ADP B 158 O1B 73.2 REMARK 620 3 ADP B 158 O1A 88.0 64.9 REMARK 620 4 HOH B 620 O 80.8 95.6 159.8 REMARK 620 5 HOH B 706 O 160.6 88.4 89.7 95.3 REMARK 620 6 HOH B 779 O 88.5 144.7 85.0 111.2 110.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF B 157 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP B 158 O3B REMARK 620 2 BEF B 157 F1 116.5 REMARK 620 3 BEF B 157 F2 106.0 107.9 REMARK 620 4 BEF B 157 F3 109.8 107.7 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BEF C 157 F1 REMARK 620 2 ADP C 158 O1B 82.0 REMARK 620 3 ADP C 158 O1A 92.3 86.4 REMARK 620 4 HOH C 643 O 78.9 159.4 86.6 REMARK 620 5 HOH C 777 O 92.0 95.4 175.5 93.0 REMARK 620 6 HOH C 778 O 170.9 98.6 78.7 99.0 97.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF C 157 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP C 158 O3B REMARK 620 2 BEF C 157 F1 116.0 REMARK 620 3 BEF C 157 F2 82.5 108.8 REMARK 620 4 BEF C 157 F3 127.1 108.2 109.9 REMARK 620 N 1 2 3 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 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 156 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF A 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF B 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF C 157 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP C 158 DBREF 2BEF A 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 2BEF B 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 2BEF C 1 155 UNP P22887 NDKC_DICDI 1 155 SEQRES 1 A 155 MET SER THR ASN LYS VAL ASN LYS GLU ARG THR PHE LEU SEQRES 2 A 155 ALA VAL LYS PRO ASP GLY VAL ALA ARG GLY LEU VAL GLY SEQRES 3 A 155 GLU ILE ILE ALA ARG TYR GLU LYS LYS GLY PHE VAL LEU SEQRES 4 A 155 VAL GLY LEU LYS GLN LEU VAL PRO THR LYS ASP LEU ALA SEQRES 5 A 155 GLU SER HIS TYR ALA GLU HIS LYS GLU ARG PRO PHE PHE SEQRES 6 A 155 GLY GLY LEU VAL SER PHE ILE THR SER GLY PRO VAL VAL SEQRES 7 A 155 ALA MET VAL PHE GLU GLY LYS GLY VAL VAL ALA SER ALA SEQRES 8 A 155 ARG LEU MET ILE GLY VAL THR ASN PRO LEU ALA SER ALA SEQRES 9 A 155 PRO GLY SER ILE ARG GLY ASP PHE GLY VAL ASP VAL GLY SEQRES 10 A 155 ARG ASN ILE ILE HIS GLY SER ASP SER VAL GLU SER ALA SEQRES 11 A 155 ASN ARG GLU ILE ALA LEU TRP PHE LYS PRO GLU GLU LEU SEQRES 12 A 155 LEU THR GLU VAL LYS PRO ASN PRO ASN LEU TYR GLU SEQRES 1 B 155 MET SER THR ASN LYS VAL ASN LYS GLU ARG THR PHE LEU SEQRES 2 B 155 ALA VAL LYS PRO ASP GLY VAL ALA ARG GLY LEU VAL GLY SEQRES 3 B 155 GLU ILE ILE ALA ARG TYR GLU LYS LYS GLY PHE VAL LEU SEQRES 4 B 155 VAL GLY LEU LYS GLN LEU VAL PRO THR LYS ASP LEU ALA SEQRES 5 B 155 GLU SER HIS TYR ALA GLU HIS LYS GLU ARG PRO PHE PHE SEQRES 6 B 155 GLY GLY LEU VAL SER PHE ILE THR SER GLY PRO VAL VAL SEQRES 7 B 155 ALA MET VAL PHE GLU GLY LYS GLY VAL VAL ALA SER ALA SEQRES 8 B 155 ARG LEU MET ILE GLY VAL THR ASN PRO LEU ALA SER ALA SEQRES 9 B 155 PRO GLY SER ILE ARG GLY ASP PHE GLY VAL ASP VAL GLY SEQRES 10 B 155 ARG ASN ILE ILE HIS GLY SER ASP SER VAL GLU SER ALA SEQRES 11 B 155 ASN ARG GLU ILE ALA LEU TRP PHE LYS PRO GLU GLU LEU SEQRES 12 B 155 LEU THR GLU VAL LYS PRO ASN PRO ASN LEU TYR GLU SEQRES 1 C 155 MET SER THR ASN LYS VAL ASN LYS GLU ARG THR PHE LEU SEQRES 2 C 155 ALA VAL LYS PRO ASP GLY VAL ALA ARG GLY LEU VAL GLY SEQRES 3 C 155 GLU ILE ILE ALA ARG TYR GLU LYS LYS GLY PHE VAL LEU SEQRES 4 C 155 VAL GLY LEU LYS GLN LEU VAL PRO THR LYS ASP LEU ALA SEQRES 5 C 155 GLU SER HIS TYR ALA GLU HIS LYS GLU ARG PRO PHE PHE SEQRES 6 C 155 GLY GLY LEU VAL SER PHE ILE THR SER GLY PRO VAL VAL SEQRES 7 C 155 ALA MET VAL PHE GLU GLY LYS GLY VAL VAL ALA SER ALA SEQRES 8 C 155 ARG LEU MET ILE GLY VAL THR ASN PRO LEU ALA SER ALA SEQRES 9 C 155 PRO GLY SER ILE ARG GLY ASP PHE GLY VAL ASP VAL GLY SEQRES 10 C 155 ARG ASN ILE ILE HIS GLY SER ASP SER VAL GLU SER ALA SEQRES 11 C 155 ASN ARG GLU ILE ALA LEU TRP PHE LYS PRO GLU GLU LEU SEQRES 12 C 155 LEU THR GLU VAL LYS PRO ASN PRO ASN LEU TYR GLU HET MG A 156 1 HET BEF A 157 4 HET ADP A 158 27 HET MG B 156 1 HET BEF B 157 4 HET ADP B 158 27 HET MG C 156 1 HET BEF C 157 4 HET ADP C 158 27 HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 4 MG 3(MG 2+) FORMUL 5 BEF 3(BE F3 1-) FORMUL 6 ADP 3(C10 H15 N5 O10 P2) FORMUL 13 HOH *220(H2 O) HELIX 1 1 PRO A 17 ALA A 21 1 5 HELIX 2 2 VAL A 25 LYS A 35 1 11 HELIX 3 3 LYS A 49 HIS A 55 1 7 HELIX 4 4 ALA A 57 HIS A 59 5 3 HELIX 5 5 PHE A 65 ILE A 72 1 8 HELIX 6 6 VAL A 87 ILE A 95 1 9 HELIX 7 7 PRO A 100 ALA A 102 5 3 HELIX 8 8 ILE A 108 PHE A 112 1 5 HELIX 9 9 VAL A 127 TRP A 137 1 11 HELIX 10 10 PRO A 140 GLU A 142 5 3 HELIX 11 11 PRO B 17 ALA B 21 1 5 HELIX 12 12 VAL B 25 LYS B 35 1 11 HELIX 13 13 LYS B 49 HIS B 55 1 7 HELIX 14 14 ALA B 57 HIS B 59 5 3 HELIX 15 15 PHE B 65 ILE B 72 1 8 HELIX 16 16 VAL B 87 ILE B 95 1 9 HELIX 17 17 PRO B 100 ALA B 102 5 3 HELIX 18 18 ILE B 108 PHE B 112 1 5 HELIX 19 19 VAL B 127 TRP B 137 1 11 HELIX 20 20 PRO B 140 GLU B 142 5 3 HELIX 21 21 PRO C 17 ALA C 21 1 5 HELIX 22 22 VAL C 25 LYS C 35 1 11 HELIX 23 23 LYS C 49 HIS C 55 1 7 HELIX 24 24 ALA C 57 HIS C 59 5 3 HELIX 25 25 PRO C 63 ILE C 72 5 10 HELIX 26 26 VAL C 87 ILE C 95 1 9 HELIX 27 27 PRO C 100 ALA C 102 5 3 HELIX 28 28 ILE C 108 PHE C 112 1 5 HELIX 29 29 VAL C 127 TRP C 137 1 11 HELIX 30 30 PRO C 140 GLU C 142 5 3 SHEET 1 A 4 ILE A 121 GLY A 123 0 SHEET 2 A 4 ARG A 10 VAL A 15 -1 N ALA A 14 O HIS A 122 SHEET 3 A 4 PRO A 76 GLU A 83 -1 N PHE A 82 O THR A 11 SHEET 4 A 4 VAL A 38 VAL A 46 -1 N LEU A 45 O VAL A 77 SHEET 1 B 4 ILE B 121 GLY B 123 0 SHEET 2 B 4 ARG B 10 VAL B 15 -1 N ALA B 14 O HIS B 122 SHEET 3 B 4 PRO B 76 GLU B 83 -1 N PHE B 82 O THR B 11 SHEET 4 B 4 VAL B 38 VAL B 46 -1 N LEU B 45 O VAL B 77 SHEET 1 C 4 ILE C 121 GLY C 123 0 SHEET 2 C 4 ARG C 10 VAL C 15 -1 N ALA C 14 O HIS C 122 SHEET 3 C 4 PRO C 76 GLU C 83 -1 N PHE C 82 O THR C 11 SHEET 4 C 4 VAL C 38 VAL C 46 -1 N LEU C 45 O VAL C 77 LINK NH2 ARG B 92 F2 BEF B 157 1555 1555 2.40 LINK OH TYR C 56 F3 BEF C 157 1555 1555 2.35 LINK F2 BEF C 157 O3B ADP C 158 1555 1555 2.30 LINK MG MG A 156 F3 BEF A 157 1555 1555 2.08 LINK MG MG A 156 O1B ADP A 158 1555 1555 2.19 LINK MG MG A 156 O1A ADP A 158 1555 1555 2.12 LINK MG MG A 156 O HOH A 619 1555 1555 2.03 LINK MG MG A 156 O HOH A 626 1555 1555 1.94 LINK MG MG A 156 O HOH A 693 1555 1555 1.90 LINK BE BEF A 157 O3B ADP A 158 1555 1555 1.88 LINK MG MG B 156 F1 BEF B 157 1555 1555 2.20 LINK MG MG B 156 O1B ADP B 158 1555 1555 2.42 LINK MG MG B 156 O1A ADP B 158 1555 1555 2.52 LINK MG MG B 156 O HOH B 620 1555 1555 2.15 LINK MG MG B 156 O HOH B 706 1555 1555 1.97 LINK MG MG B 156 O HOH B 779 1555 1555 2.02 LINK BE BEF B 157 O3B ADP B 158 1555 1555 1.87 LINK MG MG C 156 F1 BEF C 157 1555 1555 2.33 LINK MG MG C 156 O1B ADP C 158 1555 1555 2.31 LINK MG MG C 156 O1A ADP C 158 1555 1555 2.10 LINK MG MG C 156 O HOH C 643 1555 1555 1.99 LINK MG MG C 156 O HOH C 777 1555 1555 1.91 LINK MG MG C 156 O HOH C 778 1555 1555 2.13 LINK BE BEF C 157 O3B ADP C 158 1555 1555 1.85 SITE 1 AC1 5 BEF A 157 ADP A 158 HOH A 619 HOH A 626 SITE 2 AC1 5 HOH A 693 SITE 1 AC2 5 BEF B 157 ADP B 158 HOH B 620 HOH B 706 SITE 2 AC2 5 HOH B 779 SITE 1 AC3 5 BEF C 157 ADP C 158 HOH C 643 HOH C 777 SITE 2 AC3 5 HOH C 778 SITE 1 AC4 10 LYS A 16 TYR A 56 ARG A 92 ARG A 109 SITE 2 AC4 10 HIS A 122 GLY A 123 MG A 156 ADP A 158 SITE 3 AC4 10 HOH A 619 HOH A 626 SITE 1 AC5 16 LYS A 16 HIS A 59 PHE A 64 LEU A 68 SITE 2 AC5 16 ARG A 92 THR A 98 ARG A 109 VAL A 116 SITE 3 AC5 16 ASN A 119 MG A 156 BEF A 157 HOH A 619 SITE 4 AC5 16 HOH A 626 HOH A 681 HOH A 693 HOH A 729 SITE 1 AC6 10 LYS B 16 TYR B 56 ARG B 92 ARG B 109 SITE 2 AC6 10 HIS B 122 GLY B 123 MG B 156 ADP B 158 SITE 3 AC6 10 HOH B 620 HOH B 779 SITE 1 AC7 15 LYS A 60 LYS B 16 HIS B 59 PHE B 64 SITE 2 AC7 15 LEU B 68 ARG B 92 THR B 98 ARG B 109 SITE 3 AC7 15 VAL B 116 ASN B 119 MG B 156 BEF B 157 SITE 4 AC7 15 HOH B 706 HOH B 779 HOH B 802 SITE 1 AC8 9 LYS C 16 TYR C 56 ARG C 109 HIS C 122 SITE 2 AC8 9 GLY C 123 MG C 156 ADP C 158 HOH C 643 SITE 3 AC8 9 HOH C 777 SITE 1 AC9 15 LYS C 16 TYR C 56 HIS C 59 PHE C 64 SITE 2 AC9 15 LEU C 68 ARG C 92 THR C 98 ARG C 109 SITE 3 AC9 15 VAL C 116 ASN C 119 MG C 156 BEF C 157 SITE 4 AC9 15 HOH C 617 HOH C 643 HOH C 778 CRYST1 71.560 71.560 153.750 90.00 90.00 120.00 P 31 2 1 18 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 0.013974 0.008068 0.000000 0.00000 SCALE2 0.000000 0.016136 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006504 0.00000