HEADER PHOSPHOTRANSFERASE 27-APR-94 1NDC TITLE X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP TITLE 2 AND MG2+ AT 2 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_TAXID: 44689 KEYWDS PHOSPHOTRANSFERASE, NUCLEOSIDE TRIPHOSPHATE, NUCLEOSIDE DIPHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR J.CHERFILS,S.MORERA,J.JANIN REVDAT 4 14-FEB-24 1NDC 1 REMARK LINK ATOM REVDAT 3 13-JUL-11 1NDC 1 VERSN REVDAT 2 24-FEB-09 1NDC 1 VERSN REVDAT 1 22-JUN-94 1NDC 0 JRNL AUTH J.CHERFILS,S.MORERA,I.LASCU,M.VERON,J.JANIN JRNL TITL X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED JRNL TITL 2 WITH THYMIDINE DIPHOSPHATE AND MG2+ AT 2-A RESOLUTION. JRNL REF BIOCHEMISTRY V. 33 9062 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 8049207 JRNL DOI 10.1021/BI00197A006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MORERA,I.LASCU,C.DUMAS,G.LEBRAS,P.BRIOZZO,M.VERON,J.JANIN REMARK 1 TITL ADP BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE REMARK 1 TITL 2 KINASE REMARK 1 REF BIOCHEMISTRY V. 33 459 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.DUMAS,I.LASCU,S.MORERA,P.GLASER,R.FOURME,V.WALLET, REMARK 1 AUTH 2 M.L.LACOMBE,M.VERON,J.JANIN REMARK 1 TITL X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE REMARK 1 REF EMBO J. V. 11 3203 1992 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13562 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) : 0.183 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 : 1147 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1NDC 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_1000175244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 39.90000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 23.03628 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 53.53333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 39.90000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 23.03628 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 53.53333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 39.90000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 23.03628 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.53333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 39.90000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 23.03628 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 53.53333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 39.90000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 23.03628 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 53.53333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 39.90000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 23.03628 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 53.53333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 46.07255 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 107.06667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 46.07255 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 107.06667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 46.07255 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 107.06667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 46.07255 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 107.06667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 46.07255 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 107.06667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 46.07255 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 107.06667 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 17740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -133.0 KCAL/MOL 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 303 LIES ON A SPECIAL POSITION. 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 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 ILE A 120 -47.25 64.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 A MG++ ION IS ASSOCIATED WITH TDP. 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 161 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYD A 160 O1A REMARK 620 2 TYD A 160 O2B 81.0 REMARK 620 3 HOH A 204 O 94.2 174.1 REMARK 620 4 HOH A 224 O 164.4 90.7 94.7 REMARK 620 5 HOH A 243 O 90.6 86.5 90.2 102.1 REMARK 620 6 HOH A 264 O 81.9 92.9 89.8 85.5 172.4 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 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD A 160 DBREF 1NDC A 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 HET MG A 161 1 HET TYD A 160 25 HETNAM MG MAGNESIUM ION HETNAM TYD THYMIDINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 TYD C10 H16 N2 O11 P2 FORMUL 4 HOH *105(H2 O) HELIX 1 1 LYS A 16 ARG A 22 1 7 HELIX 2 2 LEU A 24 GLY A 36 1 13 HELIX 3 3 THR A 48 TYR A 56 1 9 HELIX 4 4 ALA A 57 LYS A 60 5 4 HELIX 5 5 PHE A 64 THR A 73 1 10 HELIX 6 6 GLY A 86 GLY A 96 1 11 HELIX 7 7 ASN A 99 SER A 103 5 5 HELIX 8 8 SER A 107 GLY A 113 1 7 HELIX 9 9 SER A 126 PHE A 138 1 13 HELIX 10 10 LYS A 139 LEU A 143 5 5 SHEET 1 A 4 VAL A 38 LEU A 45 0 SHEET 2 A 4 VAL A 77 GLU A 83 -1 N VAL A 77 O LEU A 45 SHEET 3 A 4 ARG A 10 VAL A 15 -1 N THR A 11 O PHE A 82 SHEET 4 A 4 ILE A 121 GLY A 123 -1 N HIS A 122 O ALA A 14 LINK O1A TYD A 160 MG MG A 161 1555 1555 2.10 LINK O2B TYD A 160 MG MG A 161 1555 1555 2.10 LINK MG MG A 161 O HOH A 204 1555 1555 1.92 LINK MG MG A 161 O HOH A 224 1555 1555 1.98 LINK MG MG A 161 O HOH A 243 1555 1555 1.96 LINK MG MG A 161 O HOH A 264 1555 1555 2.09 SITE 1 AC1 5 TYD A 160 HOH A 204 HOH A 224 HOH A 243 SITE 2 AC1 5 HOH A 264 SITE 1 AC2 19 LYS A 16 HIS A 59 ARG A 62 PHE A 64 SITE 2 AC2 19 LEU A 68 ARG A 92 THR A 98 ARG A 109 SITE 3 AC2 19 VAL A 116 ASN A 119 MG A 161 HOH A 204 SITE 4 AC2 19 HOH A 224 HOH A 232 HOH A 243 HOH A 246 SITE 5 AC2 19 HOH A 264 HOH A 270 HOH A 284 CRYST1 79.800 79.800 160.600 90.00 90.00 120.00 H 3 2 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 0.012531 0.007235 0.000000 0.00000 SCALE2 0.000000 0.014470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006227 0.00000