10 20 30 40 50 60 70 80 1QTM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 28-JUN-99 1QTM
TITLE DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT TITLE 2 OF DNA POLYMERASE I FROM THERMUS AQUATICUS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*AP*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 7 3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA POLYMERASE I; COMPND 12 CHAIN: A; COMPND 13 FRAGMENT: KLENOW FRAGMENT, RESIDUES 293-831; COMPND 14 EC: 2.7.7.7; COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 7 ORGANISM_TAXID: 271; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PWB254
KEYWDS PROTEIN-DNA COMPLEX, CLOSED, DDTTP, POLYMERASE/DNA, KEYWDS 2 TRANSFERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.LI,V.MITAXOV,G.WAKSMAN
REVDAT 5 24-FEB-09 1QTM 1 VERSN REVDAT 4 01-APR-03 1QTM 1 JRNL REVDAT 3 26-SEP-01 1QTM 1 HELIX SHEET REVDAT 2 10-JAN-00 1QTM 1 HETNAM REVDAT 1 16-AUG-99 1QTM 0
JRNL AUTH Y.LI,V.MITAXOV,G.WAKSMAN JRNL TITL STRUCTURE-BASED DESIGN OF TAQ DNA POLYMERASES WITH JRNL TITL 2 IMPROVED PROPERTIES OF DIDEOXYNUCLEOTIDE JRNL TITL 3 INCORPORATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 9491 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10449720 JRNL DOI 10.1073/PNAS.96.17.9491
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 264278.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 25649 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) : 0.227 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1299 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3704 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 228 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4186 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.50 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.92 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) : 0.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.650 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.630 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.39 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.PA REMARK 3 PARAMETER FILE 2 : DN REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_DDT_ REMARK 3 TOPOLOGY FILE 3 : WATER.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 1QTM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB009252.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-98 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 RU200 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 IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25950 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 10.400 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 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) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.26100 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM ACETATE, PEG 4000, REMARK 280 MNCL2, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K
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 30.06700 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 60.13400 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 60.13400 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 30.06700 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 GLU A 295 CG CD OE1 OE2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 421 CG CD OE1 OE2 REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 ARG A 523 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 ASN A 627 CG OD1 ND2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 634 CG CD OE1 OE2 REMARK 470 GLU A 687 CG CD OE1 OE2 REMARK 470 GLU A 688 CG CD OE1 OE2 REMARK 470 GLU A 694 CG CD OE1 OE2 REMARK 470 ARG A 695 CG CD NE CZ NH1 NH2 REMARK 470 SER A 699 OG REMARK 470 ARG A 704 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 709 CG CD CE NZ REMARK 470 GLU A 713 CG CD OE1 OE2 REMARK 470 ARG A 716 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 774 CG CD OE1 OE2 REMARK 470 GLU A 794 CG CD OE1 OE2
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 DC B 111 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 PRO A 579 C - N - CA ANGL. DEV. = -13.4 DEGREES REMARK 500 PRO A 579 C - N - CD ANGL. DEV. = 15.3 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 LEU A 294 92.95 166.80 REMARK 500 TRP A 299 -67.68 -17.12 REMARK 500 PRO A 300 90.30 -34.89 REMARK 500 PRO A 382 -7.44 -57.91 REMARK 500 THR A 399 -163.41 -108.80 REMARK 500 GLU A 421 108.83 -56.58 REMARK 500 VAL A 433 -74.43 -126.41 REMARK 500 HIS A 480 147.95 -173.96 REMARK 500 ASP A 496 -64.99 -99.88 REMARK 500 TYR A 545 -55.89 -124.93 REMARK 500 ASP A 578 -125.28 55.49 REMARK 500 VAL A 586 -22.15 -163.55 REMARK 500 GLU A 652 5.53 -50.92 REMARK 500 ALA A 683 36.90 75.89 REMARK 500 ASP A 732 0.99 -60.14 REMARK 500 HIS A 784 -54.02 69.99 REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TTP A 113
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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 611 O REMARK 620 2 ASP A 785 OD2 88.5 REMARK 620 3 TTP A 113 O2B 97.3 80.6 REMARK 620 4 ASP A 610 OD2 80.1 75.5 155.9 REMARK 620 5 TTP A 113 O2A 171.9 86.5 75.6 104.7 REMARK 620 6 TTP A 113 O3B 98.0 137.3 56.7 147.3 81.5 REMARK 620 7 TTP A 113 O1G 118.3 149.8 107.4 94.6 68.3 57.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 785 OD1 REMARK 620 2 ASP A 610 OD1 106.0 REMARK 620 3 TTP A 113 O2A 79.6 92.9 REMARK 620 4 HOH A3008 O 157.6 89.2 83.3 REMARK 620 5 HOH A3055 O 97.4 102.9 164.0 95.0 REMARK 620 N 1 2 3 4
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 1001 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1002 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A 113
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 DDCTP-TRAPPED CLOSED TERNARY COMPLEX OF KLENTAQ
DBREF 1QTM A 293 831 UNP P19821 DPO1_THEAQ 293 831 DBREF 1QTM B 101 112 PDB 1QTM 1QTM 101 112 DBREF 1QTM C 203 216 PDB 1QTM 1QTM 203 216
SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC 2DT SEQRES 1 C 14 DA DA DA DG DC DG DC DC DG DT DG DG DT SEQRES 2 C 14 DC SEQRES 1 A 539 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 539 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 539 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 539 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 539 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 539 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 539 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 539 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 539 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 539 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 539 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 539 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 539 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 539 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 539 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 539 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 539 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 539 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 539 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 539 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 539 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 539 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 539 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 539 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 539 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 539 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 539 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 539 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 539 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 539 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 539 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 539 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 539 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 539 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 539 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 539 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 539 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 539 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 539 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 539 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 539 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 539 ASP TRP LEU SER ALA LYS
MODRES 1QTM 2DT B 112 DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
HET 2DT B 112 19 HET MG A1001 1 HET MG A1002 1 HET TTP A 113 28
HETNAM 2DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE
HETSYN 2DT 2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE
FORMUL 1 2DT C10 H15 N2 O7 P FORMUL 4 MG 2(MG 2+) FORMUL 6 TTP C10 H17 N2 O14 P3 FORMUL 7 HOH *165(H2 O)
HELIX 1 1 GLU A 337 ARG A 343 1 7 HELIX 2 2 LEU A 352 GLU A 363 1 12 HELIX 3 3 ASP A 372 ASP A 381 1 10 HELIX 4 4 THR A 386 GLY A 395 1 10 HELIX 5 5 GLU A 401 LEU A 420 1 20 HELIX 6 6 GLU A 423 VAL A 433 1 11 HELIX 7 7 VAL A 433 GLY A 448 1 16 HELIX 8 8 ASP A 452 GLY A 479 1 28 HELIX 9 9 SER A 486 ASP A 496 1 11 HELIX 10 10 SER A 515 LEU A 522 1 8 HELIX 11 11 PRO A 527 TYR A 545 1 19 HELIX 12 12 PRO A 548 LEU A 552 5 5 HELIX 13 13 THR A 588 ARG A 596 1 9 HELIX 14 14 GLN A 613 GLY A 624 1 12 HELIX 15 15 ASP A 625 GLU A 634 1 10 HELIX 16 16 ASP A 637 GLY A 648 1 12 HELIX 17 17 PRO A 650 VAL A 654 5 5 HELIX 18 18 ASP A 655 TYR A 671 1 17 HELIX 19 19 SER A 674 ALA A 683 1 10 HELIX 20 20 PRO A 685 PHE A 700 1 16 HELIX 21 21 PHE A 700 GLY A 718 1 19 HELIX 22 22 PRO A 731 ALA A 735 5 5 HELIX 23 23 VAL A 737 MET A 775 1 39 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 ASP A 826 LYS A 831 1 6
SHEET 1 A 4 GLU A 295 PRO A 298 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 N VAL A 332 O GLU A 295 SHEET 3 A 4 LEU A 321 ARG A 328 -1 O ALA A 326 N HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 O PHE A 306 N ALA A 327 SHEET 1 B 3 ARG A 559 LEU A 560 0 SHEET 2 B 3 VAL A 449 LEU A 451 -1 O VAL A 449 N LEU A 560 SHEET 3 B 3 PHE A 598 ILE A 599 -1 N ILE A 599 O ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 N VAL A 788 O LEU A 781 SHEET 3 D 4 TRP A 604 TYR A 611 -1 O LEU A 605 N ALA A 791 SHEET 4 D 4 VAL A 819 GLY A 824 -1 N GLU A 820 O ASP A 610 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 N ARG A 728 O VAL A 720
LINK MG MG A1001 O TYR A 611 1555 1555 2.22 LINK MG MG A1001 OD2 ASP A 785 1555 1555 2.15 LINK MG MG A1001 O2B TTP A 113 1555 1555 2.25 LINK MG MG A1001 OD2 ASP A 610 1555 1555 2.23 LINK MG MG A1001 O2A TTP A 113 1555 1555 2.39 LINK MG MG A1001 O3B TTP A 113 1555 1555 2.89 LINK MG MG A1001 O1G TTP A 113 1555 1555 2.22 LINK MG MG A1002 OD1 ASP A 785 1555 1555 2.32 LINK MG MG A1002 OD1 ASP A 610 1555 1555 2.61 LINK MG MG A1002 O2A TTP A 113 1555 1555 2.43 LINK MG MG A1002 O HOH A3008 1555 1555 2.48 LINK MG MG A1002 O HOH A3055 1555 1555 2.35 LINK O3' DC B 111 P 2DT B 112 1555 1555 1.61
SITE 1 AC1 4 TTP A 113 ASP A 610 TYR A 611 ASP A 785 SITE 1 AC2 6 TTP A 113 ASP A 610 ASP A 785 HOH A3008 SITE 2 AC2 6 HOH A3055 2DT B 112 SITE 1 AC3 18 ASP A 610 TYR A 611 SER A 612 GLN A 613 SITE 2 AC3 18 ILE A 614 GLU A 615 HIS A 639 ARG A 659 SITE 3 AC3 18 LYS A 663 PHE A 667 ASP A 785 MG A1001 SITE 4 AC3 18 MG A1002 HOH A3008 HOH A3043 2DT B 112 SITE 5 AC3 18 DA C 204 DA C 205
CRYST1 107.988 107.988 90.201 90.00 90.00 120.00 P 31 2 1 6
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 0.009260 0.005346 0.000000 0.00000
SCALE2 0.000000 0.010693 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011086 0.00000