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 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 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 CONECT 3424 3428 3431 3436 3514 CONECT 3424 3515 3516 CONECT 3425 3426 3427 3428 3429 CONECT 3426 3425 CONECT 3427 3425 CONECT 3428 3424 3425 CONECT 3429 3425 3430 CONECT 3430 3429 3431 3432 3433 CONECT 3431 3424 3430 CONECT 3432 3430 CONECT 3433 3430 3434 CONECT 3434 3433 3435 3436 3437 CONECT 3435 3434 CONECT 3436 3424 3434 CONECT 3437 3434 3438 CONECT 3438 3437 3439 CONECT 3439 3438 3440 3452 CONECT 3440 3439 3441 CONECT 3441 3440 3442 3450 CONECT 3442 3441 3443 3449 CONECT 3443 3442 3447 CONECT 3444 3445 CONECT 3445 3444 3446 3447 CONECT 3446 3445 CONECT 3447 3443 3445 3448 CONECT 3448 3447 3449 CONECT 3449 3442 3448 CONECT 3450 3441 3451 3452 CONECT 3451 3450 CONECT 3452 3439 3450 3453 CONECT 3453 3452 CONECT 3454 3455 3456 3457 3458 CONECT 3455 3454 CONECT 3456 3454 CONECT 3457 3454 3512 CONECT 3458 3454 3459 CONECT 3459 3458 3460 3461 3462 CONECT 3460 3459 3512 CONECT 3461 3459 CONECT 3462 3459 3463 CONECT 3463 3462 3464 3465 3466 CONECT 3464 3463 CONECT 3465 3463 3512 CONECT 3466 3463 3467 CONECT 3467 3466 3468 CONECT 3468 3467 3469 3481 CONECT 3469 3468 3470 CONECT 3470 3469 3471 3479 CONECT 3471 3470 3472 3478 CONECT 3472 3471 3476 CONECT 3473 3474 CONECT 3474 3473 3475 3476 CONECT 3475 3474 CONECT 3476 3472 3474 3477 CONECT 3477 3476 3478 CONECT 3478 3471 3477 CONECT 3479 3470 3480 3481 CONECT 3480 3479 CONECT 3481 3468 3479 3482 CONECT 3482 3481 CONECT 3483 3484 3485 3486 3487 CONECT 3484 3483 CONECT 3485 3483 CONECT 3486 3483 3513 CONECT 3487 3483 3488 CONECT 3488 3487 3489 3490 3491 CONECT 3489 3488 3513 CONECT 3490 3488 CONECT 3491 3488 3492 CONECT 3492 3491 3493 3494 3495 CONECT 3493 3492 CONECT 3494 3492 3513 CONECT 3495 3492 3496 CONECT 3496 3495 3497 CONECT 3497 3496 3498 3510 CONECT 3498 3497 3499 CONECT 3499 3498 3500 3508 CONECT 3500 3499 3501 3507 CONECT 3501 3500 3505 CONECT 3502 3503 CONECT 3503 3502 3504 3505 CONECT 3504 3503 CONECT 3505 3501 3503 3506 CONECT 3506 3505 3507 CONECT 3507 3500 3506 CONECT 3508 3499 3509 3510 CONECT 3509 3508 CONECT 3510 3497 3508 3511 CONECT 3511 3510 CONECT 3512 3457 3460 3465 3519 CONECT 3513 3486 3489 3494 CONECT 3514 3424 CONECT 3515 3424 CONECT 3516 3424 CONECT 3519 3512 MASTER 374 0 6 31 12 0 15 6 3548 3 95 36 END