HEADER TRANSFERASE/DNA 31-DEC-04 1YFH
TITLE WT HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING
TITLE 2 AN ALKYLATED CYTOSINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-
COMPND 3 3';
COMPND 4 CHAIN: D, F;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3';
COMPND 8 CHAIN: E, G;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE;
COMPND 12 CHAIN: A, B, C;
COMPND 13 SYNONYM: 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE, MGMT, O-6-
COMPND 14 METHYLGUANINE-DNA-ALKYLTRANSFERASE;
COMPND 15 EC: 2.1.1.63;
COMPND 16 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 3 23-AUG-23 1YFH 1 REMARK LINK
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 DNA AND ITS
JRNL TITL 2 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 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) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110
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. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-05.
REMARK 100 THE DEPOSITION ID IS D_1000031455.
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 -X
REMARK 300 +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
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 302
REMARK 800
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 B 303 1
HET ZN C 302 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