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 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) : 2.05 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.88 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 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 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 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: NDPK + MGADP + ALF3, WITH MGADP AND ALF3 REMOVED REMARK 200 FROM THE MODEL 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 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 LYS C 60 23.1 L L OUTSIDE RANGE 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 A 799 DISTANCE = 5.01 ANGSTROMS REMARK 525 HOH A 811 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH B 800 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH C 816 DISTANCE = 5.93 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 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 MG B 156 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BEF B 157 F1 REMARK 620 2 HOH B 706 O 160.6 REMARK 620 3 ADP B 158 O1B 73.2 88.4 REMARK 620 4 ADP B 158 O1A 88.0 89.7 64.9 REMARK 620 5 HOH B 620 O 80.8 95.3 95.6 159.8 REMARK 620 6 HOH B 779 O 88.5 110.5 144.7 85.0 111.2 REMARK 620 N 1 2 3 4 5 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 778 O 170.9 98.6 78.7 99.0 REMARK 620 6 HOH C 777 O 92.0 95.4 175.5 93.0 97.0 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 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 MG B 156 1 HET MG C 156 1 HET BEF A 157 4 HET ADP A 158 27 HET BEF B 157 4 HET ADP B 158 27 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 7 BEF 3(BE F3 1-) FORMUL 8 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 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 B 156 F1 BEF B 157 1555 1555 2.20 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 BE BEF A 157 O3B ADP A 158 1555 1555 1.88 LINK BE BEF B 157 O3B ADP B 158 1555 1555 1.87 LINK F2 BEF B 157 NH2 ARG B 92 1555 1555 2.40 LINK BE BEF C 157 O3B ADP C 158 1555 1555 1.85 LINK F2 BEF C 157 O3B ADP C 158 1555 1555 2.30 LINK F3 BEF C 157 OH TYR C 56 1555 1555 2.35 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 MG MG B 156 O HOH B 706 1555 1555 1.97 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 779 1555 1555 2.02 LINK MG MG C 156 O HOH C 643 1555 1555 1.99 LINK MG MG C 156 O HOH C 778 1555 1555 2.13 LINK MG MG C 156 O HOH C 777 1555 1555 1.91 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