10 20 30 40 50 60 70 80 1YFH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE/DNA 31-DEC-04 1YFH
TITLE WT HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA TITLE 2 CONTAINING AN ALKYLATED CYTOSINE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY) COMPND 3 P*GP*TP*GP*TP*AP*GP*GP*T)-3'; COMPND 4 CHAIN: D, F; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'- COMPND 8 D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'; COMPND 9 CHAIN: E, G; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: METHYLATED-DNA--PROTEIN-CYSTEINE COMPND 13 METHYLTRANSFERASE; COMPND 14 CHAIN: A, B, C; COMPND 15 SYNONYM: 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE, MGMT, O- COMPND 16 6-METHYLGUANINE-DNA-ALKYLTRANSFERASE; COMPND 17 EC: 2.1.1.63; COMPND 18 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: OLIGONUCLEOTIDE SYNTHESIZED BY AUTOMATED SOURCE 4 PHOSPHORAMIDITE TECHNIQUE CONTAINING UNATURAL BASE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: OLIGONUCLEOTIDE SYNTHESIZED BY AUTOMATED SOURCE 8 PHOSPHORAMIDITE TECHNIQUE; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: MGMT; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-2
KEYWDS PROTEIN-DNA COMPLEX, TRANSFERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.M.DUGUID,P.A.RICE,C.HE
REVDAT 2 24-FEB-09 1YFH 1 VERSN REVDAT 1 13-DEC-05 1YFH 0
JRNL AUTH E.M.DUGUID,P.A.RICE,C.HE JRNL TITL THE STRUCTURE OF THE HUMAN AGT PROTEIN BOUND TO JRNL TITL 2 DNA AND ITS IMPLICATIONS FOR DAMAGE DETECTION. JRNL REF J.MOL.BIOL. V. 350 657 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15964013 JRNL DOI 10.1016/J.JMB.2005.05.028
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 628363.490 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 17404 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) : 0.246 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 835 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 3.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2101 REMARK 3 BIN R VALUE (WORKING SET) : 0.4150 REMARK 3 BIN FREE R VALUE : 0.4770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 94 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.049 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3621 REMARK 3 NUCLEIC ACID ATOMS : 1316 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.14000 REMARK 3 B22 (A**2) : -33.90000 REMARK 3 B33 (A**2) : 20.76000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 19.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM SIGMAA (A) : 0.85 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) : 0.58 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.92 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.11 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP 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 : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 26.73 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : DNA_CSTAR.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : DNA_CSTAR.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1YFH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031455.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .900 REMARK 200 MONOCHROMATOR : BENT GE (111) REMARK 200 OPTICS : BENT CONICAL SI-MIRROR (RH REMARK 200 COATING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19448 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 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) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1T38 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CHLORIDE, CITRATE, REMARK 280 MAGNESIUM CHLORIDE, PH 5.7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 51.35500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 DNA BOUND TO MONOMER B IS COMPLETED BY TWO FOLD AXIS REMARK 300 -X +1, Y +.5, -Z +2.
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: D, E, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, G, 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 ASP A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 36 REMARK 465 GLY A 37 REMARK 465 THR A 38 REMARK 465 SER A 39 REMARK 465 ALA A 40 REMARK 465 ALA A 41 REMARK 465 ASP A 42 REMARK 465 ALA A 43 REMARK 465 VAL A 44 REMARK 465 GLU A 45 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 LYS B 3 REMARK 465 ASP B 4 REMARK 465 LYS B 36 REMARK 465 GLY B 37 REMARK 465 THR B 38 REMARK 465 SER B 39 REMARK 465 ALA B 40 REMARK 465 ALA B 41 REMARK 465 ASP B 42 REMARK 465 ALA B 43 REMARK 465 VAL B 44 REMARK 465 GLU B 45 REMARK 465 LEU B 176 REMARK 465 GLY B 177 REMARK 465 LYS B 178 REMARK 465 PRO B 179 REMARK 465 MET C 1 REMARK 465 ASP C 2 REMARK 465 LYS C 3 REMARK 465 ASP C 4 REMARK 465 LYS C 36 REMARK 465 GLY C 37 REMARK 465 THR C 38 REMARK 465 SER C 39 REMARK 465 ALA C 40 REMARK 465 ALA C 41 REMARK 465 ASP C 42 REMARK 465 ALA C 43 REMARK 465 VAL C 44 REMARK 465 GLU C 45 REMARK 465 VAL C 46 REMARK 465 PRO C 47 REMARK 465 ALA C 48 REMARK 465 PRO C 49 REMARK 465 ALA C 50 REMARK 465 ALA C 51 REMARK 465 VAL C 52 REMARK 465 LEU C 53 REMARK 465 GLY C 54 REMARK 465 GLY C 156 REMARK 465 ASN C 157 REMARK 465 TYR C 158 REMARK 465 SER C 159 REMARK 465 GLY C 160 REMARK 465 LYS C 178 REMARK 465 PRO C 179
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 CYS A 24 -150.85 -104.24 REMARK 500 GLU A 30 141.98 -171.57 REMARK 500 PRO A 56 164.55 -44.29 REMARK 500 GLN A 72 41.70 174.03 REMARK 500 PRO A 73 -11.98 -48.36 REMARK 500 PRO A 87 -36.40 -39.05 REMARK 500 VAL A 106 98.69 -67.06 REMARK 500 ALA A 127 -47.32 -29.52 REMARK 500 ILE A 141 -44.86 65.80 REMARK 500 PRO A 144 77.89 -53.88 REMARK 500 LEU A 162 -54.46 -25.21 REMARK 500 LYS A 178 74.51 -111.28 REMARK 500 GLU B 6 103.45 -45.78 REMARK 500 CYS B 24 -150.95 -104.61 REMARK 500 GLU B 30 145.03 -170.19 REMARK 500 PRO B 47 68.23 -67.55 REMARK 500 ALA B 48 138.86 -36.63 REMARK 500 PRO B 49 157.10 -43.28 REMARK 500 GLN B 72 36.85 -152.31 REMARK 500 PRO B 73 -26.04 -39.22 REMARK 500 PRO B 87 -35.82 -39.08 REMARK 500 SER B 93 157.27 176.65 REMARK 500 VAL B 105 -73.04 -83.71 REMARK 500 VAL B 106 94.66 -56.69 REMARK 500 ILE B 141 -47.14 69.06 REMARK 500 PRO B 144 75.85 -56.46 REMARK 500 SER B 152 35.74 -91.52 REMARK 500 ASN B 157 -157.34 -102.97 REMARK 500 TYR B 158 139.80 171.36 REMARK 500 THR C 10 136.70 -179.07 REMARK 500 CYS C 24 -147.83 -105.69 REMARK 500 GLU C 30 144.07 -171.35 REMARK 500 GLN C 72 39.65 170.35 REMARK 500 PRO C 73 -3.20 -52.21 REMARK 500 GLU C 77 -8.16 -58.35 REMARK 500 PRO C 87 -30.72 -37.35 REMARK 500 GLN C 91 144.60 -175.11 REMARK 500 VAL C 105 -70.85 -80.82 REMARK 500 VAL C 106 97.47 -64.83 REMARK 500 ALA C 126 32.97 -98.86 REMARK 500 ILE C 141 -47.84 72.09 REMARK 500 PRO C 144 78.92 -54.19 REMARK 500 SER C 151 7.50 -68.98 REMARK 500 ALA C 154 157.87 -47.06 REMARK 500 LEU C 176 -140.38 -97.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC G 15 0.07 SIDE_CHAIN 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 HIS A 29 NE2 136.4 REMARK 620 3 HIS A 85 ND1 99.1 103.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 5 SG REMARK 620 2 HIS B 29 NE2 72.9 REMARK 620 3 HIS B 85 ND1 89.9 87.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 5 SG REMARK 620 2 CYS C 24 SG 145.1 REMARK 620 3 HIS C 29 NE2 82.8 114.5 REMARK 620 4 HIS C 85 ND1 97.9 113.8 82.2 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 302 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 303
DBREF 1YFH A 1 179 UNP P16455 MGMT_HUMAN 1 179 DBREF 1YFH B 1 179 UNP P16455 MGMT_HUMAN 1 179 DBREF 1YFH C 1 179 UNP P16455 MGMT_HUMAN 1 179 DBREF 1YFH D 1 16 PDB 1YFH 1YFH 1 16 DBREF 1YFH E 15 -1 PDB 1YFH 1YFH 15 -1 DBREF 1YFH F 1 16 PDB 1YFH 1YFH 1 16 DBREF 1YFH G 15 -1 PDB 1YFH 1YFH 15 -1
SEQRES 1 D 16 DG DT DG DG DA DT DG XCY DG DT DG DT DA SEQRES 2 D 16 DG DG DT SEQRES 1 E 16 DC DC DT DA DC DA DC DA DC DA DT DC DC SEQRES 2 E 16 DA DC DA SEQRES 1 F 16 DG DT DG DG DA DT DG XCY DG DT DG DT DA SEQRES 2 F 16 DG DG DT SEQRES 1 G 16 DC DC DT DA DC DA DC DA DC DA DT DC DC SEQRES 2 G 16 DA DC DA SEQRES 1 A 179 MET ASP LYS ASP CYS GLU MET LYS ARG THR THR LEU ASP SEQRES 2 A 179 SER PRO LEU GLY LYS LEU GLU LEU SER GLY CYS GLU GLN SEQRES 3 A 179 GLY LEU HIS GLU ILE LYS LEU LEU GLY LYS GLY THR SER SEQRES 4 A 179 ALA ALA ASP ALA VAL GLU VAL PRO ALA PRO ALA ALA VAL SEQRES 5 A 179 LEU GLY GLY PRO GLU PRO LEU MET GLN CYS THR ALA TRP SEQRES 6 A 179 LEU ASN ALA TYR PHE HIS GLN PRO GLU ALA ILE GLU GLU SEQRES 7 A 179 PHE PRO VAL PRO ALA LEU HIS HIS PRO VAL PHE GLN GLN SEQRES 8 A 179 GLU SER PHE THR ARG GLN VAL LEU TRP LYS LEU LEU LYS SEQRES 9 A 179 VAL VAL LYS PHE GLY GLU VAL ILE SER TYR GLN GLN LEU SEQRES 10 A 179 ALA ALA LEU ALA GLY ASN PRO LYS ALA ALA ARG ALA VAL SEQRES 11 A 179 GLY GLY ALA MET ARG GLY ASN PRO VAL PRO ILE LEU ILE SEQRES 12 A 179 PRO CYS HIS ARG VAL VAL CYS SER SER GLY ALA VAL GLY SEQRES 13 A 179 ASN TYR SER GLY GLY LEU ALA VAL LYS GLU TRP LEU LEU SEQRES 14 A 179 ALA HIS GLU GLY HIS ARG LEU GLY LYS PRO SEQRES 1 B 179 MET ASP LYS ASP CYS GLU MET LYS ARG THR THR LEU ASP SEQRES 2 B 179 SER PRO LEU GLY LYS LEU GLU LEU SER GLY CYS GLU GLN SEQRES 3 B 179 GLY LEU HIS GLU ILE LYS LEU LEU GLY LYS GLY THR SER SEQRES 4 B 179 ALA ALA ASP ALA VAL GLU VAL PRO ALA PRO ALA ALA VAL SEQRES 5 B 179 LEU GLY GLY PRO GLU PRO LEU MET GLN CYS THR ALA TRP SEQRES 6 B 179 LEU ASN ALA TYR PHE HIS GLN PRO GLU ALA ILE GLU GLU SEQRES 7 B 179 PHE PRO VAL PRO ALA LEU HIS HIS PRO VAL PHE GLN GLN SEQRES 8 B 179 GLU SER PHE THR ARG GLN VAL LEU TRP LYS LEU LEU LYS SEQRES 9 B 179 VAL VAL LYS PHE GLY GLU VAL ILE SER TYR GLN GLN LEU SEQRES 10 B 179 ALA ALA LEU ALA GLY ASN PRO LYS ALA ALA ARG ALA VAL SEQRES 11 B 179 GLY GLY ALA MET ARG GLY ASN PRO VAL PRO ILE LEU ILE SEQRES 12 B 179 PRO CYS HIS ARG VAL VAL CYS SER SER GLY ALA VAL GLY SEQRES 13 B 179 ASN TYR SER GLY GLY LEU ALA VAL LYS GLU TRP LEU LEU SEQRES 14 B 179 ALA HIS GLU GLY HIS ARG LEU GLY LYS PRO SEQRES 1 C 179 MET ASP LYS ASP CYS GLU MET LYS ARG THR THR LEU ASP SEQRES 2 C 179 SER PRO LEU GLY LYS LEU GLU LEU SER GLY CYS GLU GLN SEQRES 3 C 179 GLY LEU HIS GLU ILE LYS LEU LEU GLY LYS GLY THR SER SEQRES 4 C 179 ALA ALA ASP ALA VAL GLU VAL PRO ALA PRO ALA ALA VAL SEQRES 5 C 179 LEU GLY GLY PRO GLU PRO LEU MET GLN CYS THR ALA TRP SEQRES 6 C 179 LEU ASN ALA TYR PHE HIS GLN PRO GLU ALA ILE GLU GLU SEQRES 7 C 179 PHE PRO VAL PRO ALA LEU HIS HIS PRO VAL PHE GLN GLN SEQRES 8 C 179 GLU SER PHE THR ARG GLN VAL LEU TRP LYS LEU LEU LYS SEQRES 9 C 179 VAL VAL LYS PHE GLY GLU VAL ILE SER TYR GLN GLN LEU SEQRES 10 C 179 ALA ALA LEU ALA GLY ASN PRO LYS ALA ALA ARG ALA VAL SEQRES 11 C 179 GLY GLY ALA MET ARG GLY ASN PRO VAL PRO ILE LEU ILE SEQRES 12 C 179 PRO CYS HIS ARG VAL VAL CYS SER SER GLY ALA VAL GLY SEQRES 13 C 179 ASN TYR SER GLY GLY LEU ALA VAL LYS GLU TRP LEU LEU SEQRES 14 C 179 ALA HIS GLU GLY HIS ARG LEU GLY LYS PRO
MODRES 1YFH XCY D 8 DC MODRES 1YFH XCY F 8 DC
HET XCY D 8 28 HET XCY F 8 28 HET ZN A 301 1 HET ZN C 302 1 HET ZN B 303 1
HETNAM XCY {5-[4-{[4-(AMINOMETHYL)BENZYL]AMINO}-2-OXOPYRIMIDIN- HETNAM 2 XCY 1(2H)- YL]-3-HYDROXYTETRAHYDROFURAN-2-YL}METHYL HETNAM 3 XCY DIHYDROGEN PHOSPHATE HETNAM ZN ZINC ION
FORMUL 1 XCY 2(C17 H23 N4 O7 P) FORMUL 8 ZN 3(ZN 2+) FORMUL 11 HOH *6(H2 O)
HELIX 1 1 PRO A 56 GLN A 72 1 17 HELIX 2 2 GLU A 74 GLU A 78 5 5 HELIX 3 3 HIS A 86 GLN A 91 1 6 HELIX 4 4 SER A 93 VAL A 106 1 14 HELIX 5 5 TYR A 114 GLY A 122 1 9 HELIX 6 6 ALA A 126 GLY A 136 1 11 HELIX 7 7 GLY A 161 GLU A 172 1 12 HELIX 8 8 PRO B 56 GLN B 72 1 17 HELIX 9 9 PRO B 73 ILE B 76 5 4 HELIX 10 10 HIS B 86 GLN B 91 1 6 HELIX 11 11 SER B 93 VAL B 105 1 13 HELIX 12 12 TYR B 114 GLY B 122 1 9 HELIX 13 13 ALA B 126 ASN B 137 1 12 HELIX 14 14 GLY B 161 GLU B 172 1 12 HELIX 15 15 PRO C 56 GLN C 72 1 17 HELIX 16 16 GLU C 74 PHE C 79 5 6 HELIX 17 17 HIS C 86 GLN C 91 5 6 HELIX 18 18 SER C 93 VAL C 106 1 14 HELIX 19 19 TYR C 114 GLY C 122 1 9 HELIX 20 20 ALA C 126 ASN C 137 1 12 HELIX 21 21 GLY C 161 GLU C 172 1 12
SHEET 1 A 3 LYS A 8 SER A 14 0 SHEET 2 A 3 GLY A 17 GLY A 23 -1 O GLY A 17 N SER A 14 SHEET 3 A 3 LEU A 28 GLY A 35 -1 O LYS A 32 N GLU A 20 SHEET 1 B 2 ILE A 112 SER A 113 0 SHEET 2 B 2 VAL A 148 VAL A 149 1 O VAL A 149 N ILE A 112 SHEET 1 C 4 LEU B 28 LEU B 33 0 SHEET 2 C 4 GLY B 17 GLY B 23 -1 N GLU B 20 O LYS B 32 SHEET 3 C 4 LYS B 8 SER B 14 -1 N SER B 14 O GLY B 17 SHEET 4 C 4 ALA B 50 ALA B 51 1 O ALA B 50 N ARG B 9 SHEET 1 D 2 ILE B 112 SER B 113 0 SHEET 2 D 2 VAL B 148 VAL B 149 1 O VAL B 149 N ILE B 112 SHEET 1 E 3 LYS C 8 SER C 14 0 SHEET 2 E 3 GLY C 17 GLY C 23 -1 O LEU C 21 N THR C 10 SHEET 3 E 3 LEU C 28 GLY C 35 -1 O LYS C 32 N GLU C 20 SHEET 1 F 2 ILE C 112 SER C 113 0 SHEET 2 F 2 VAL C 148 VAL C 149 1 O VAL C 149 N ILE C 112
LINK O3' DG D 7 P XCY D 8 1555 1555 1.60 LINK O3' XCY D 8 P DG D 9 1555 1555 1.61 LINK O3' DG F 7 P XCY F 8 1555 1555 1.60 LINK O3' XCY F 8 P DG F 9 1555 1555 1.61 LINK SG CYS A 24 ZN ZN A 301 1555 1555 2.41 LINK NE2 HIS A 29 ZN ZN A 301 1555 1555 1.90 LINK ND1 HIS A 85 ZN ZN A 301 1555 1555 1.95 LINK SG CYS B 5 ZN ZN B 303 1555 1555 2.57 LINK NE2 HIS B 29 ZN ZN B 303 1555 1555 2.27 LINK ND1 HIS B 85 ZN ZN B 303 1555 1555 1.97 LINK SG CYS C 5 ZN ZN C 302 1555 1555 2.19 LINK SG CYS C 24 ZN ZN C 302 1555 1555 2.09 LINK NE2 HIS C 29 ZN ZN C 302 1555 1555 2.31 LINK ND1 HIS C 85 ZN ZN C 302 1555 1555 1.89
SITE 1 AC1 5 CYS A 5 MET A 7 CYS A 24 HIS A 29 SITE 2 AC1 5 HIS A 85 SITE 1 AC2 4 CYS C 5 CYS C 24 HIS C 29 HIS C 85 SITE 1 AC3 5 CYS B 5 MET B 7 CYS B 24 HIS B 29 SITE 2 AC3 5 HIS B 85
CRYST1 58.150 102.710 87.940 90.00 106.77 90.00 P 1 21 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 0.017197 0.000000 0.005182 0.00000
SCALE2 0.000000 0.009736 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011876 0.00000