HEADER TRANSFERASE 05-SEP-02 1MN9 TITLE NDP KINASE MUTANT (H122G) COMPLEX WITH RTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NDP KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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 KEYWDS NDP KINASE-RIBAVIRIN COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GALLOIS-MONTBRUN,Y.CHEN,H.DUTARTRE,S.MORERA,C.GUERREIRO,L.MULARD, AUTHOR 2 B.SCHNEIDER,J.JANIN,B.CANARD,M.VERON,D.DEVILLE-BONNE REVDAT 5 29-MAY-24 1MN9 1 REMARK REVDAT 4 10-NOV-21 1MN9 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1MN9 1 VERSN REVDAT 2 24-FEB-09 1MN9 1 VERSN REVDAT 1 18-MAR-03 1MN9 0 JRNL AUTH S.GALLOIS-MONTBRUN,Y.CHEN,H.DUTARTRE,M.SOPHYS,S.MORERA, JRNL AUTH 2 C.GUERREIRO,B.SCHNEIDER,L.MULARD,J.JANIN,M.VERON, JRNL AUTH 3 D.DEVILLE-BONNE,B.CANARD JRNL TITL STRUCTURAL ANALYSIS OF THE ACTIVATION OF RIBAVIRIN ANALOGS JRNL TITL 2 BY NDP KINASE: COMPARISON WITH OTHER RIBAVIRIN TARGETS JRNL REF MOL.PHARMACOL. V. 63 538 2003 JRNL REFN ISSN 0026-895X JRNL PMID 12606760 JRNL DOI 10.1124/MOL.63.3.538 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.20 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10546 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 553 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 : 3420 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 38 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1MN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-01 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10546 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 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) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11700 REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550, TRIS-HCL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 51.27267 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 102.54533 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 102.54533 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 51.27267 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 BIOLOGICAL ASSEMBLY IS A HEXAMER GENERATED FROM THE REMARK 300 TRIMER IN THE ASYMMETRIC UNIT 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: 18360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 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 -0.500000 -0.866025 0.000000 107.59650 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 62.12087 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.27267 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: 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 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG B 92 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 92 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG C 92 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG C 92 NE - CZ - NH2 ANGL. DEV. = 3.6 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 39.08 -77.89 REMARK 500 TYR A 56 31.41 -89.62 REMARK 500 LYS A 60 -16.34 -49.85 REMARK 500 PRO A 63 1.16 -51.55 REMARK 500 ILE A 72 -10.14 -48.97 REMARK 500 ILE A 120 -48.51 55.64 REMARK 500 ALA A 130 -71.27 -63.03 REMARK 500 ASP B 50 -70.12 -64.38 REMARK 500 ILE B 72 -11.06 -49.21 REMARK 500 VAL B 114 -17.85 -140.77 REMARK 500 ILE B 120 -49.17 54.24 REMARK 500 ALA B 130 -71.04 -62.93 REMARK 500 ASN C 7 81.38 -150.13 REMARK 500 GLU C 9 135.03 -38.72 REMARK 500 TYR C 56 31.74 -88.72 REMARK 500 ILE C 72 -9.72 -50.54 REMARK 500 ARG C 118 71.01 -119.41 REMARK 500 ILE C 120 -49.52 56.11 REMARK 500 ALA C 130 -71.86 -63.28 REMARK 500 PRO C 151 2.31 -69.32 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 164 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 RTP A 160 O2A REMARK 620 2 RTP A 160 O1B 81.0 REMARK 620 3 RTP A 160 O3G 71.8 84.9 REMARK 620 4 HOH A1001 O 79.4 143.1 59.3 REMARK 620 5 HOH A1002 O 142.5 75.0 77.7 103.3 REMARK 620 6 HOH A1003 O 108.9 74.6 158.9 141.7 92.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 163 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 RTP A 161 O2A REMARK 620 2 RTP A 161 O3G 110.2 REMARK 620 3 RTP A 161 O1B 70.8 77.4 REMARK 620 4 HOH A1016 O 98.2 111.1 54.8 REMARK 620 N 1 2 3 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 RTP A 162 O3G REMARK 620 2 RTP A 162 O2A 64.3 REMARK 620 3 RTP A 162 O1B 79.6 75.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 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 RTP A 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RTP A 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RTP A 162 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F3F RELATED DB: PDB REMARK 900 1F3F CONTAINS THE SAME PROTEIN COMPLEXED WITH D4T-TRIPHOSPHATE AND REMARK 900 MG REMARK 900 RELATED ID: 1NUE RELATED DB: PDB REMARK 900 1NUE CONTAINS HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH REMARK 900 GDP DBREF 1MN9 A 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 1MN9 B 1 155 UNP P22887 NDKC_DICDI 1 155 DBREF 1MN9 C 1 155 UNP P22887 NDKC_DICDI 1 155 SEQADV 1MN9 GLY A 122 UNP P22887 HIS 122 ENGINEERED MUTATION SEQADV 1MN9 GLY B 122 UNP P22887 HIS 122 ENGINEERED MUTATION SEQADV 1MN9 GLY C 122 UNP P22887 HIS 122 ENGINEERED MUTATION 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 GLY 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 GLY 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 GLY 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 164 1 HET RTP A 160 29 HET RTP A 161 29 HET RTP A 162 29 HET MG B 163 1 HET MG C 165 1 HETNAM MG MAGNESIUM ION HETNAM RTP RIBAVIRIN TRIPHOSPHATE FORMUL 4 MG 3(MG 2+) FORMUL 5 RTP 3(C8 H15 N4 O14 P3) FORMUL 10 HOH *38(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 ILE A 72 1 9 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 ASP A 115 ASN A 119 5 5 HELIX 10 10 SER A 126 PHE A 138 1 13 HELIX 11 11 LYS A 139 LEU A 143 5 5 HELIX 12 12 LYS B 16 ARG B 22 1 7 HELIX 13 13 LEU B 24 GLY B 36 1 13 HELIX 14 14 THR B 48 TYR B 56 1 9 HELIX 15 15 ALA B 57 LYS B 60 5 4 HELIX 16 16 PHE B 64 ILE B 72 1 9 HELIX 17 17 GLY B 86 GLY B 96 1 11 HELIX 18 18 ASN B 99 SER B 103 5 5 HELIX 19 19 SER B 107 GLY B 113 1 7 HELIX 20 20 SER B 126 PHE B 138 1 13 HELIX 21 21 LYS B 139 LEU B 143 5 5 HELIX 22 22 LYS C 16 ARG C 22 1 7 HELIX 23 23 LEU C 24 GLY C 36 1 13 HELIX 24 24 THR C 48 TYR C 56 1 9 HELIX 25 25 ALA C 57 LYS C 60 5 4 HELIX 26 26 PHE C 64 ILE C 72 1 9 HELIX 27 27 GLY C 86 GLY C 96 1 11 HELIX 28 28 ASN C 99 SER C 103 5 5 HELIX 29 29 SER C 107 GLY C 113 1 7 HELIX 30 30 SER C 126 PHE C 138 1 13 HELIX 31 31 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 GLU A 83 N VAL A 38 SHEET 3 A 4 ARG A 10 VAL A 15 -1 N LEU A 13 O MET A 80 SHEET 4 A 4 ILE A 121 GLY A 123 -1 O GLY A 122 N 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 O VAL B 81 N GLY B 41 SHEET 3 B 4 ARG B 10 VAL B 15 -1 N LEU B 13 O MET B 80 SHEET 4 B 4 ILE B 121 GLY B 123 -1 O GLY 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 O VAL C 81 N GLY C 41 SHEET 3 C 4 ARG C 10 VAL C 15 -1 N LEU C 13 O MET C 80 SHEET 4 C 4 ILE C 121 GLY C 123 -1 O GLY C 122 N ALA C 14 LINK O2A RTP A 160 MG MG A 164 1555 1555 2.17 LINK O1B RTP A 160 MG MG A 164 1555 1555 2.41 LINK O3G RTP A 160 MG MG A 164 1555 1555 2.78 LINK O2A RTP A 161 MG MG B 163 1555 1555 1.89 LINK O3G RTP A 161 MG MG B 163 1555 1555 1.99 LINK O1B RTP A 161 MG MG B 163 1555 1555 2.83 LINK O3G RTP A 162 MG MG C 165 1555 1555 2.68 LINK O2A RTP A 162 MG MG C 165 1555 1555 2.26 LINK O1B RTP A 162 MG MG C 165 1555 1555 2.46 LINK MG MG A 164 O HOH A1001 1555 1555 1.92 LINK MG MG A 164 O HOH A1002 1555 1555 2.01 LINK MG MG A 164 O HOH A1003 1555 1555 1.94 LINK O HOH A1016 MG MG B 163 1555 1555 1.90 SITE 1 AC1 2 RTP A 161 HOH A1016 SITE 1 AC2 4 RTP A 160 HOH A1001 HOH A1002 HOH A1003 SITE 1 AC3 2 RTP A 162 ASP C 125 SITE 1 AC4 16 LYS A 16 TYR A 56 HIS A 59 PHE A 64 SITE 2 AC4 16 LEU A 68 ARG A 92 THR A 98 ARG A 109 SITE 3 AC4 16 VAL A 116 ASN A 119 GLY A 122 GLY A 123 SITE 4 AC4 16 MG A 164 HOH A1001 HOH A1002 HOH A1003 SITE 1 AC5 14 HOH A1016 LYS B 16 TYR B 56 HIS B 59 SITE 2 AC5 14 PHE B 64 LEU B 68 ARG B 92 THR B 98 SITE 3 AC5 14 ARG B 109 VAL B 116 ASN B 119 GLY B 122 SITE 4 AC5 14 GLY B 123 MG B 163 SITE 1 AC6 13 LYS C 16 TYR C 56 HIS C 59 PHE C 64 SITE 2 AC6 13 LEU C 68 ARG C 92 THR C 98 ARG C 109 SITE 3 AC6 13 VAL C 116 ASN C 119 GLY C 122 GLY C 123 SITE 4 AC6 13 MG C 165 CRYST1 71.731 71.731 153.818 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 0.013941 0.008049 0.000000 0.00000 SCALE2 0.000000 0.016098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006501 0.00000