HEADER TRANSFERASE 23-JUN-00 1F6T TITLE STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE); COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NDK, NDP KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES 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; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTZ18R KEYWDS NUCLEOSIDE DIPHOSPHATE KINASE, ANTI-HIV NUCLEOSIDE ANALOGUE, KEYWDS 2 PHOSPHORYLATION, BORANOPHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.GUERREIRO,J.BORETTO,J.JANIN,M.VERON,B.CANARD,B.SCHNEIDER,S.SARFATI, AUTHOR 2 D.DEVILLE-BONNE REVDAT 4 07-FEB-24 1F6T 1 REMARK LINK REVDAT 3 13-JUL-11 1F6T 1 VERSN REVDAT 2 24-FEB-09 1F6T 1 VERSN REVDAT 1 13-SEP-00 1F6T 0 JRNL AUTH P.MEYER,B.SCHNEIDER,S.SARFATI,D.DEVILLE-BONNE,C.GUERREIRO, JRNL AUTH 2 J.BORETTO,J.JANIN,M.VERON,B.CANARD JRNL TITL STRUCTURAL BASIS FOR ACTIVATION OF ALPHA-BORANOPHOSPHATE JRNL TITL 2 NUCLEOTIDE ANALOGUES TARGETING DRUG-RESISTANT REVERSE JRNL TITL 3 TRANSCRIPTASE. JRNL REF EMBO J. V. 19 3520 2000 JRNL REFN ISSN 0261-4189 JRNL PMID 10899107 JRNL DOI 10.1093/EMBOJ/19.14.3520 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 33430 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) : 0.228 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1378 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4514 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 200 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 377 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 0.73000 REMARK 3 B12 (A**2) : 0.24000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 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) : 1.640 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.300 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 50.58 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : BTDP_DNA-RNA_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 : BTDP_DNA-RNA.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 1F6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.10500 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50 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 51.26400 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 102.52800 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 102.52800 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 51.26400 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: 18160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 121.86536 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 102.52800 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 MET C 1 REMARK 465 SER C 2 REMARK 465 THR C 3 REMARK 465 ASN C 4 REMARK 465 LYS C 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 5 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE C 138 O HOH C 564 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 OE2 GLU B 61 OE2 GLU B 61 6555 2.05 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 ILE A 120 N - CA - C ANGL. DEV. = 16.2 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 ASN A 7 2.61 -59.88 REMARK 500 LYS A 43 147.44 -174.08 REMARK 500 VAL A 114 -9.51 -140.28 REMARK 500 ILE A 120 -40.57 59.77 REMARK 500 LEU B 42 135.33 -175.70 REMARK 500 VAL B 114 -2.76 -153.02 REMARK 500 ASN B 119 30.22 -99.57 REMARK 500 ILE B 120 -44.29 64.17 REMARK 500 ASN C 7 20.54 -66.32 REMARK 500 LYS C 43 147.63 -175.30 REMARK 500 TYR C 56 41.19 -92.51 REMARK 500 PRO C 63 -75.11 -57.88 REMARK 500 PHE C 64 -16.69 -34.85 REMARK 500 VAL C 114 -28.79 -144.86 REMARK 500 ARG C 118 54.97 -111.86 REMARK 500 ASN C 119 32.80 -87.02 REMARK 500 ILE C 120 -41.49 54.27 REMARK 500 SER C 124 165.83 -44.33 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 163 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TBD A 160 O2A REMARK 620 2 TBD A 160 O2B 79.8 REMARK 620 3 HOH A 775 O 96.8 90.7 REMARK 620 4 HOH A 776 O 89.7 162.8 104.1 REMARK 620 5 HOH A 872 O 147.4 87.9 113.5 94.0 REMARK 620 6 HOH A 875 O 77.1 77.6 167.5 86.9 70.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 164 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TBD B 161 O2B REMARK 620 2 TBD B 161 O2A 78.5 REMARK 620 3 HOH B 782 O 89.8 81.4 REMARK 620 4 HOH B 869 O 84.7 89.4 170.1 REMARK 620 5 HOH B 870 O 165.1 86.9 84.7 98.5 REMARK 620 6 HOH B 871 O 102.1 176.3 94.9 94.3 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 165 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TBD C 162 O2A REMARK 620 2 TBD C 162 O2B 52.6 REMARK 620 3 HOH C 800 O 69.1 62.8 REMARK 620 4 HOH C 863 O 120.8 76.3 61.6 REMARK 620 5 HOH C 873 O 49.3 96.0 109.2 169.9 REMARK 620 6 HOH C 876 O 89.2 62.1 122.9 91.4 90.6 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 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBD A 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBD B 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBD C 162 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F3F RELATED DB: PDB REMARK 900 1F3F IS NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX REMARK 900 RELATED ID: 1LWX RELATED DB: PDB REMARK 900 1LWX IS NUCLEOSIDE DIPHOSPHATE KINASE / AZT-DIPHOSPHATE COMPLEX DBREF 1F6T A 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 1F6T B 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 1F6T 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 163 1 HET TBD A 160 25 HET MG B 164 1 HET TBD B 161 25 HET MG C 165 1 HET TBD C 162 25 HETNAM MG MAGNESIUM ION HETNAM TBD 2*-DEOXY-THYMIDINE-5*-ALPHA BORANO DIPHOSPHATE (ISOMER HETNAM 2 TBD RP) FORMUL 4 MG 3(MG 2+) FORMUL 5 TBD 3(C10 H19 B N2 O10 P2) FORMUL 10 HOH *377(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 HELIX 11 11 LYS B 16 ARG B 22 1 7 HELIX 12 12 LEU B 24 GLY B 36 1 13 HELIX 13 13 THR B 48 TYR B 56 1 9 HELIX 14 14 ALA B 57 LYS B 60 5 4 HELIX 15 15 PHE B 64 THR B 73 1 10 HELIX 16 16 GLY B 86 GLY B 96 1 11 HELIX 17 17 ASN B 99 SER B 103 5 5 HELIX 18 18 SER B 107 GLY B 113 1 7 HELIX 19 19 SER B 126 PHE B 138 1 13 HELIX 20 20 LYS B 139 LEU B 143 5 5 HELIX 21 21 LYS C 16 ARG C 22 1 7 HELIX 22 22 LEU C 24 GLY C 36 1 13 HELIX 23 23 THR C 48 TYR C 56 1 9 HELIX 24 24 PHE C 64 THR C 73 1 10 HELIX 25 25 GLY C 86 GLY C 96 1 11 HELIX 26 26 ASN C 99 SER C 103 5 5 HELIX 27 27 SER C 107 GLY C 113 1 7 HELIX 28 28 SER C 126 PHE C 138 1 13 HELIX 29 29 LYS C 139 LEU C 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 O VAL A 77 N 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 SHEET 1 B 4 VAL B 38 LEU B 45 0 SHEET 2 B 4 VAL B 77 GLU B 83 -1 N VAL B 77 O LEU B 45 SHEET 3 B 4 ARG B 10 VAL B 15 -1 N THR B 11 O PHE B 82 SHEET 4 B 4 ILE B 121 GLY B 123 -1 O HIS B 122 N ALA B 14 SHEET 1 C 4 VAL C 38 LEU C 45 0 SHEET 2 C 4 VAL C 77 GLU C 83 -1 N VAL C 77 O LEU C 45 SHEET 3 C 4 ARG C 10 VAL C 15 -1 N THR C 11 O PHE C 82 SHEET 4 C 4 ILE C 121 GLY C 123 -1 O HIS C 122 N ALA C 14 LINK O2A TBD A 160 MG MG A 163 1555 1555 2.26 LINK O2B TBD A 160 MG MG A 163 1555 1555 2.24 LINK MG MG A 163 O HOH A 775 1555 1555 2.19 LINK MG MG A 163 O HOH A 776 1555 1555 2.36 LINK MG MG A 163 O HOH A 872 1555 1555 2.28 LINK MG MG A 163 O HOH A 875 1555 1555 2.27 LINK O2B TBD B 161 MG MG B 164 1555 1555 2.20 LINK O2A TBD B 161 MG MG B 164 1555 1555 2.26 LINK MG MG B 164 O HOH B 782 1555 1555 2.39 LINK MG MG B 164 O HOH B 869 1555 1555 2.31 LINK MG MG B 164 O HOH B 870 1555 1555 2.29 LINK MG MG B 164 O HOH B 871 1555 1555 2.18 LINK O2A TBD C 162 MG MG C 165 1555 1555 2.79 LINK O2B TBD C 162 MG MG C 165 1555 1555 2.81 LINK MG MG C 165 O HOH C 800 1555 1555 2.54 LINK MG MG C 165 O HOH C 863 1555 1555 2.70 LINK MG MG C 165 O HOH C 873 1555 1555 2.77 LINK MG MG C 165 O HOH C 876 1555 1555 2.29 SITE 1 AC1 6 ARG A 92 TBD A 160 HOH A 775 HOH A 776 SITE 2 AC1 6 HOH A 872 HOH A 875 SITE 1 AC2 6 ARG B 92 TBD B 161 HOH B 782 HOH B 869 SITE 2 AC2 6 HOH B 870 HOH B 871 SITE 1 AC3 7 GLU C 58 ARG C 92 TBD C 162 HOH C 800 SITE 2 AC3 7 HOH C 863 HOH C 873 HOH C 876 SITE 1 AC4 18 LYS A 16 TYR A 56 HIS A 59 PHE A 64 SITE 2 AC4 18 LEU A 68 ARG A 92 THR A 98 ARG A 109 SITE 3 AC4 18 VAL A 116 GLY A 117 ASN A 119 MG A 163 SITE 4 AC4 18 HOH A 563 HOH A 615 HOH A 669 HOH A 712 SITE 5 AC4 18 HOH A 875 HOH B 797 SITE 1 AC5 15 LYS B 16 HIS B 59 PHE B 64 LEU B 68 SITE 2 AC5 15 ARG B 92 THR B 98 ARG B 109 VAL B 116 SITE 3 AC5 15 GLY B 117 ASN B 119 MG B 164 HOH B 572 SITE 4 AC5 15 HOH B 632 HOH B 782 HOH B 869 SITE 1 AC6 18 LYS C 16 HIS C 59 PHE C 64 LEU C 68 SITE 2 AC6 18 ARG C 92 THR C 98 ARG C 109 VAL C 116 SITE 3 AC6 18 GLY C 117 ASN C 119 MG C 165 HOH C 559 SITE 4 AC6 18 HOH C 565 HOH C 676 HOH C 800 HOH C 827 SITE 5 AC6 18 HOH C 873 HOH C 876 CRYST1 70.359 70.359 153.792 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 0.014213 0.008206 0.000000 0.00000 SCALE2 0.000000 0.016412 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006502 0.00000