HEADER HYDROLASE/HYDROLASE INHIBITOR 02-JUL-18 6DYV TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI 5'-METHYLTHIOADENOSINE/S- TITLE 2 ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH (3R,4S)-1- TITLE 3 ((4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL)-4-((PENT-4-YN-1- TITLE 4 YLTHIO)METHYL)PYRROLIDIN-3-OL COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.2.2.9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 210; SOURCE 5 GENE: BW246_00770, BZL55_04980, CEP79_03920; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MTAN ENZYME, DUODENAL ULCERS, STOMACH CANCER, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.K.HARIJAN,R.G.DUCATI,J.B.BONANNO,S.C.ALMO,V.L.SCHRAMM REVDAT 4 11-OCT-23 6DYV 1 REMARK REVDAT 3 24-APR-19 6DYV 1 JRNL REVDAT 2 10-APR-19 6DYV 1 JRNL REVDAT 1 20-MAR-19 6DYV 0 JRNL AUTH R.K.HARIJAN,O.HOFF,R.G.DUCATI,R.S.FIRESTONE,B.M.HIRSCH, JRNL AUTH 2 G.B.EVANS,V.L.SCHRAMM,P.C.TYLER JRNL TITL SELECTIVE INHIBITORS OF HELICOBACTER PYLORI JRNL TITL 2 METHYLTHIOADENOSINE NUCLEOSIDASE AND HUMAN JRNL TITL 3 METHYLTHIOADENOSINE PHOSPHORYLASE. JRNL REF J. MED. CHEM. V. 62 3286 2019 JRNL REFN ISSN 1520-4804 JRNL PMID 30860833 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01642 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 58317 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 + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3055 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3707 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3525 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 477 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.704 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3734 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3562 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5028 ; 1.553 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8285 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 5.607 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;31.816 ;25.646 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 657 ;13.036 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.931 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 582 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4124 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 706 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1894 ; 1.173 ; 1.892 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1893 ; 1.172 ; 1.891 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2378 ; 1.811 ; 2.832 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2379 ; 1.811 ; 2.833 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1838 ; 1.915 ; 2.177 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1839 ; 1.915 ; 2.177 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2651 ; 2.980 ; 3.155 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4278 ; 4.785 ;24.561 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4279 ; 4.784 ;24.562 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A -1 230 B -1 230 14720 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6DYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235451. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 88.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4WKP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.5, 20% W/V PEG8000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.10250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.73950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.73950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.05125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.73950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.73950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 132.15375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.73950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.73950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.05125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.73950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.73950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 132.15375 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.10250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -88.10250 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 -73.47900 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 -73.47900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -88.10250 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 436 LIES ON A SPECIAL POSITION. 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 -14 REMARK 465 GLY A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 MET B -14 REMARK 465 GLY B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 GLU B -6 REMARK 465 ASN B -5 REMARK 465 LEU B -4 REMARK 465 TYR B -3 REMARK 465 PHE B -2 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 LYS A 84 CD CE NZ REMARK 470 LYS A 157 CD CE NZ REMARK 470 GLN B -1 CG CD OE1 NE2 REMARK 470 LYS B 84 CD CE NZ REMARK 470 LYS B 133 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 471 O HOH A 490 1.97 REMARK 500 O HOH B 592 O HOH B 614 2.03 REMARK 500 O2 EDO B 304 O HOH B 401 2.05 REMARK 500 NE2 GLN A 184 O HOH A 401 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O2 EDO B 302 O2 EDO B 302 8444 2.00 REMARK 500 O2 EDO A 304 O2 EDO A 304 8554 2.04 REMARK 500 ND2 ASN A 42 O HIS B 41 8454 2.06 REMARK 500 O HIS A 41 ND2 ASN B 42 8454 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 MET A 64 CG - SD - CE ANGL. DEV. = -15.7 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 HIS A 41 -131.66 52.25 REMARK 500 ASN A 42 30.59 -97.01 REMARK 500 LYS A 51 162.64 85.42 REMARK 500 ASN A 89 -14.42 82.91 REMARK 500 SER A 117 -149.82 -136.36 REMARK 500 HIS A 155 45.56 -149.50 REMARK 500 GLU A 175 -24.90 -146.40 REMARK 500 ASP A 201 -169.31 -115.98 REMARK 500 HIS B 41 -130.90 51.42 REMARK 500 ASN B 42 30.27 -95.93 REMARK 500 LYS B 51 161.57 86.32 REMARK 500 ASN B 89 -14.40 83.29 REMARK 500 SER B 117 -151.59 -136.89 REMARK 500 HIS B 155 47.15 -149.37 REMARK 500 GLU B 175 -25.38 -145.49 REMARK 500 ASP B 201 -169.34 -115.21 REMARK 500 ASP B 201 -168.02 -115.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OS3 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OS3 B 305 DBREF1 6DYV A 1 230 UNP A0A1W0VQJ9_HELPX DBREF2 6DYV A A0A1W0VQJ9 2 231 DBREF1 6DYV B 1 230 UNP A0A1W0VQJ9_HELPX DBREF2 6DYV B A0A1W0VQJ9 2 231 SEQADV 6DYV MET A -14 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLY A -13 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS A -12 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS A -11 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS A -10 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS A -9 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS A -8 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS A -7 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLU A -6 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV ASN A -5 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV LEU A -4 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV TYR A -3 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV PHE A -2 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLN A -1 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLY A 0 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV MET B -14 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLY B -13 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS B -12 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS B -11 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS B -10 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS B -9 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS B -8 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV HIS B -7 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLU B -6 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV ASN B -5 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV LEU B -4 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV TYR B -3 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV PHE B -2 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLN B -1 UNP A0A1W0VQJ EXPRESSION TAG SEQADV 6DYV GLY B 0 UNP A0A1W0VQJ EXPRESSION TAG SEQRES 1 A 245 MET GLY HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE SEQRES 2 A 245 GLN GLY VAL GLN LYS ILE GLY ILE LEU GLY ALA MET ARG SEQRES 3 A 245 GLU GLU ILE THR PRO ILE LEU GLU LEU PHE GLY VAL ASP SEQRES 4 A 245 PHE GLU GLU ILE PRO LEU GLY GLY ASN VAL PHE HIS LYS SEQRES 5 A 245 GLY VAL TYR HIS ASN LYS GLU ILE ILE VAL ALA TYR SER SEQRES 6 A 245 LYS ILE GLY LYS VAL HIS SER THR LEU THR THR THR SER SEQRES 7 A 245 MET ILE LEU ALA PHE GLY VAL GLN LYS VAL LEU PHE SER SEQRES 8 A 245 GLY VAL ALA GLY SER LEU VAL LYS ASP LEU LYS ILE ASN SEQRES 9 A 245 ASP LEU LEU VAL ALA THR GLN LEU VAL GLN HIS ASP VAL SEQRES 10 A 245 ASP LEU SER ALA PHE ASP HIS PRO LEU GLY PHE ILE PRO SEQRES 11 A 245 GLU SER ALA ILE PHE ILE GLU THR SER GLY SER LEU ASN SEQRES 12 A 245 ALA LEU ALA LYS LYS ILE ALA ASN GLU GLN HIS ILE ALA SEQRES 13 A 245 LEU LYS GLU GLY VAL ILE ALA SER GLY ASP GLN PHE VAL SEQRES 14 A 245 HIS SER LYS GLU ARG LYS GLU PHE LEU VAL SER GLU PHE SEQRES 15 A 245 LYS ALA SER ALA VAL GLU MET GLU GLY ALA SER VAL ALA SEQRES 16 A 245 PHE VAL CYS GLN LYS PHE GLY VAL PRO CYS CYS VAL LEU SEQRES 17 A 245 ARG SER ILE SER ASP ASN ALA ASP GLU LYS ALA GLY MET SEQRES 18 A 245 SER PHE ASP GLU PHE LEU GLU LYS SER ALA HIS THR SER SEQRES 19 A 245 ALA LYS PHE LEU LYS SER MET VAL ASP GLU LEU SEQRES 1 B 245 MET GLY HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE SEQRES 2 B 245 GLN GLY VAL GLN LYS ILE GLY ILE LEU GLY ALA MET ARG SEQRES 3 B 245 GLU GLU ILE THR PRO ILE LEU GLU LEU PHE GLY VAL ASP SEQRES 4 B 245 PHE GLU GLU ILE PRO LEU GLY GLY ASN VAL PHE HIS LYS SEQRES 5 B 245 GLY VAL TYR HIS ASN LYS GLU ILE ILE VAL ALA TYR SER SEQRES 6 B 245 LYS ILE GLY LYS VAL HIS SER THR LEU THR THR THR SER SEQRES 7 B 245 MET ILE LEU ALA PHE GLY VAL GLN LYS VAL LEU PHE SER SEQRES 8 B 245 GLY VAL ALA GLY SER LEU VAL LYS ASP LEU LYS ILE ASN SEQRES 9 B 245 ASP LEU LEU VAL ALA THR GLN LEU VAL GLN HIS ASP VAL SEQRES 10 B 245 ASP LEU SER ALA PHE ASP HIS PRO LEU GLY PHE ILE PRO SEQRES 11 B 245 GLU SER ALA ILE PHE ILE GLU THR SER GLY SER LEU ASN SEQRES 12 B 245 ALA LEU ALA LYS LYS ILE ALA ASN GLU GLN HIS ILE ALA SEQRES 13 B 245 LEU LYS GLU GLY VAL ILE ALA SER GLY ASP GLN PHE VAL SEQRES 14 B 245 HIS SER LYS GLU ARG LYS GLU PHE LEU VAL SER GLU PHE SEQRES 15 B 245 LYS ALA SER ALA VAL GLU MET GLU GLY ALA SER VAL ALA SEQRES 16 B 245 PHE VAL CYS GLN LYS PHE GLY VAL PRO CYS CYS VAL LEU SEQRES 17 B 245 ARG SER ILE SER ASP ASN ALA ASP GLU LYS ALA GLY MET SEQRES 18 B 245 SER PHE ASP GLU PHE LEU GLU LYS SER ALA HIS THR SER SEQRES 19 B 245 ALA LYS PHE LEU LYS SER MET VAL ASP GLU LEU HET EDO A 301 4 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET OS3 A 306 24 HET EDO B 301 4 HET EDO B 302 4 HET EDO B 303 4 HET EDO B 304 4 HET OS3 B 305 24 HETNAM EDO 1,2-ETHANEDIOL HETNAM OS3 (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL) HETNAM 2 OS3 METHYL]-4-{[(PENT-4-YN-1-YL) HETNAM 3 OS3 SULFANYL]METHYL}PYRROLIDIN-3-OL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 9(C2 H6 O2) FORMUL 8 OS3 2(C17 H23 N5 O S) FORMUL 14 HOH *477(H2 O) HELIX 1 AA1 MET A 10 GLY A 22 1 13 HELIX 2 AA2 GLY A 53 GLY A 69 1 17 HELIX 3 AA3 LEU A 104 ASP A 108 5 5 HELIX 4 AA4 SER A 124 HIS A 139 1 16 HELIX 5 AA5 SER A 156 LYS A 168 1 13 HELIX 6 AA6 GLU A 175 GLY A 187 1 13 HELIX 7 AA7 LYS A 203 ASP A 228 1 26 HELIX 8 AA8 MET B 10 GLY B 22 1 13 HELIX 9 AA9 GLY B 53 GLY B 69 1 17 HELIX 10 AB1 LEU B 104 ASP B 108 5 5 HELIX 11 AB2 SER B 124 HIS B 139 1 16 HELIX 12 AB3 SER B 156 LYS B 168 1 13 HELIX 13 AB4 GLU B 175 GLY B 187 1 13 HELIX 14 AB5 LYS B 203 ASP B 228 1 26 SHEET 1 AA1 9 GLU A 26 LEU A 30 0 SHEET 2 AA1 9 ASN A 33 TYR A 40 -1 O PHE A 35 N ILE A 28 SHEET 3 AA1 9 LYS A 43 TYR A 49 -1 O VAL A 47 N HIS A 36 SHEET 4 AA1 9 GLN A 2 GLY A 8 1 N GLN A 2 O GLU A 44 SHEET 5 AA1 9 LYS A 72 SER A 81 1 O LYS A 72 N GLY A 5 SHEET 6 AA1 9 ALA A 169 GLU A 173 -1 O VAL A 172 N GLY A 80 SHEET 7 AA1 9 LEU A 142 SER A 149 1 N VAL A 146 O SER A 170 SHEET 8 AA1 9 LEU A 91 GLN A 99 1 N VAL A 98 O SER A 149 SHEET 9 AA1 9 ILE A 121 GLU A 122 -1 O ILE A 121 N LEU A 97 SHEET 1 AA2 8 GLU A 26 LEU A 30 0 SHEET 2 AA2 8 ASN A 33 TYR A 40 -1 O PHE A 35 N ILE A 28 SHEET 3 AA2 8 LYS A 43 TYR A 49 -1 O VAL A 47 N HIS A 36 SHEET 4 AA2 8 GLN A 2 GLY A 8 1 N GLN A 2 O GLU A 44 SHEET 5 AA2 8 LYS A 72 SER A 81 1 O LYS A 72 N GLY A 5 SHEET 6 AA2 8 CYS A 190 ASP A 198 1 O CYS A 191 N PHE A 75 SHEET 7 AA2 8 LEU A 91 GLN A 99 -1 N LEU A 92 O ARG A 194 SHEET 8 AA2 8 ILE A 121 GLU A 122 -1 O ILE A 121 N LEU A 97 SHEET 1 AA3 9 GLU B 26 LEU B 30 0 SHEET 2 AA3 9 ASN B 33 TYR B 40 -1 O PHE B 35 N ILE B 28 SHEET 3 AA3 9 LYS B 43 TYR B 49 -1 O VAL B 47 N HIS B 36 SHEET 4 AA3 9 GLN B 2 GLY B 8 1 N GLN B 2 O GLU B 44 SHEET 5 AA3 9 LYS B 72 SER B 81 1 O LYS B 72 N GLY B 5 SHEET 6 AA3 9 ALA B 171 GLU B 173 -1 O VAL B 172 N GLY B 80 SHEET 7 AA3 9 LEU B 142 SER B 149 1 N ALA B 148 O ALA B 171 SHEET 8 AA3 9 LEU B 91 GLN B 99 1 N VAL B 98 O SER B 149 SHEET 9 AA3 9 PHE B 120 GLU B 122 -1 O ILE B 121 N LEU B 97 SHEET 1 AA4 8 GLU B 26 LEU B 30 0 SHEET 2 AA4 8 ASN B 33 TYR B 40 -1 O PHE B 35 N ILE B 28 SHEET 3 AA4 8 LYS B 43 TYR B 49 -1 O VAL B 47 N HIS B 36 SHEET 4 AA4 8 GLN B 2 GLY B 8 1 N GLN B 2 O GLU B 44 SHEET 5 AA4 8 LYS B 72 SER B 81 1 O LYS B 72 N GLY B 5 SHEET 6 AA4 8 CYS B 190 ASP B 198 1 O ASP B 198 N SER B 81 SHEET 7 AA4 8 LEU B 91 GLN B 99 -1 N LEU B 92 O ARG B 194 SHEET 8 AA4 8 PHE B 120 GLU B 122 -1 O ILE B 121 N LEU B 97 SITE 1 AC1 8 SER A 124 GLY A 125 SER A 126 HOH A 406 SITE 2 AC1 8 HOH A 560 PHE B 107 ASP B 209 OS3 B 305 SITE 1 AC2 5 GLY A 32 ASN A 33 VAL A 34 TYR A 49 SITE 2 AC2 5 HOH A 438 SITE 1 AC3 5 GLN A 138 HIS A 139 SER A 165 GLU A 166 SITE 2 AC3 5 HOH A 541 SITE 1 AC4 2 ARG A 159 HOH A 463 SITE 1 AC5 5 LYS A 157 GLU A 158 GLU A 161 HOH A 439 SITE 2 AC5 5 GLU B 202 SITE 1 AC6 19 ALA A 9 MET A 10 ILE A 52 VAL A 78 SITE 2 AC6 19 ALA A 79 GLY A 80 LEU A 104 PHE A 107 SITE 3 AC6 19 GLN A 152 PHE A 153 VAL A 154 GLU A 173 SITE 4 AC6 19 MET A 174 GLU A 175 SER A 197 ASP A 198 SITE 5 AC6 19 ALA A 200 PHE A 208 HOH A 420 SITE 1 AC7 5 GLY B 32 ASN B 33 VAL B 34 TYR B 49 SITE 2 AC7 5 HOH B 462 SITE 1 AC8 3 GLN B 152 ARG B 159 HOH B 515 SITE 1 AC9 7 SER A 126 ALA B 106 MET B 206 HOH B 413 SITE 2 AC9 7 HOH B 435 HOH B 457 HOH B 591 SITE 1 AD1 7 GLN A 71 LYS A 72 PRO A 189 HOH A 403 SITE 2 AD1 7 GLU B 210 HOH B 401 HOH B 466 SITE 1 AD2 19 EDO A 301 ALA B 9 ILE B 52 VAL B 78 SITE 2 AD2 19 ALA B 79 GLY B 80 LEU B 104 PHE B 153 SITE 3 AD2 19 VAL B 154 VAL B 172 GLU B 173 MET B 174 SITE 4 AD2 19 GLU B 175 SER B 197 ASP B 198 ALA B 200 SITE 5 AD2 19 PHE B 208 ASP B 209 HOH B 426 CRYST1 73.479 73.479 176.205 90.00 90.00 90.00 P 41 21 2 16 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 0.013609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005675 0.00000