HEADER TRANSFERASE 02-JUL-18 6DYZ TITLE CRYSTAL STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE TITLE 2 PHOSPHORYLASE IN COMPLEX WITH (3R,4S)-1-((4-AMINO-5H-PYRROLO[3,2- TITLE 3 D]PYRIMIDIN-7-YL)METHYL)-4-((PROP-2-YN-1-YLTHIO)METHYL)PYRROLIDIN-3- TITLE 4 OL COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-METHYL-5'-THIOADENOSINE PHOSPHORYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE, MTAPASE; COMPND 5 EC: 2.4.2.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MTAP, MSAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MTAP ENZYME, CANCER, PHOSPHORYLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.HARIJAN,R.G.DUCATI,J.B.BONANNO,S.C.ALMO,V.L.SCHRAMM REVDAT 5 11-OCT-23 6DYZ 1 REMARK REVDAT 4 04-DEC-19 6DYZ 1 REMARK REVDAT 3 24-APR-19 6DYZ 1 JRNL REVDAT 2 10-APR-19 6DYZ 1 JRNL REVDAT 1 20-MAR-19 6DYZ 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) : 106.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 46245 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2268 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) : 3336 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 1.60000 REMARK 3 B12 (A**2) : -0.25000 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): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.629 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2220 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2099 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3006 ; 1.573 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4883 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 6.302 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;34.854 ;24.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 391 ;12.214 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.656 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 345 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2416 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 429 ; 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): 1105 ; 1.424 ; 1.974 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1104 ; 1.418 ; 1.972 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1384 ; 2.279 ; 2.955 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1385 ; 2.279 ; 2.958 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1115 ; 2.209 ; 2.291 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1116 ; 2.208 ; 2.290 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1621 ; 3.560 ; 3.311 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2564 ; 5.589 ;25.509 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2565 ; 5.588 ;25.503 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 NUMBER OF DIFFERENT NCS GROUPS : NULL 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 6DYZ 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_1000235455. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 48526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 106.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.0000 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 5TC6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.0, 10% W/V PEG6000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 0.00000 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 0.00000 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 0.00000 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 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 -0.500000 -0.866025 0.000000 122.82100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 61.41050 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 106.36611 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 CL CL A 301 LIES ON A SPECIAL POSITION. REMARK 375 CL CL A 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 495 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 606 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 -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 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 THR A 6 REMARK 465 THR A 7 REMARK 465 THR A 8 REMARK 465 ARG A 282 REMARK 465 HIS A 283 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 464 O HOH A 595 2.15 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 O HOH A 417 O HOH A 417 5556 1.63 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 ARG A 60 NE - CZ - NH1 ANGL. DEV. = 3.2 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 20 39.88 -145.16 REMARK 500 LYS A 51 -124.39 52.05 REMARK 500 TYR A 125 73.77 -101.08 REMARK 500 ASP A 222 -122.32 51.56 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 CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OS2 A 307 DBREF 6DYZ A 1 283 UNP Q13126 MTAP_HUMAN 1 283 SEQADV 6DYZ MET A -13 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ HIS A -12 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ HIS A -11 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ HIS A -10 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ HIS A -9 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ HIS A -8 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ HIS A -7 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ GLU A -6 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ ASN A -5 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ LEU A -4 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ TYR A -3 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ PHE A -2 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ GLN A -1 UNP Q13126 EXPRESSION TAG SEQADV 6DYZ SER A 0 UNP Q13126 EXPRESSION TAG SEQRES 1 A 297 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 A 297 SER MET ALA SER GLY THR THR THR THR ALA VAL LYS ILE SEQRES 3 A 297 GLY ILE ILE GLY GLY THR GLY LEU ASP ASP PRO GLU ILE SEQRES 4 A 297 LEU GLU GLY ARG THR GLU LYS TYR VAL ASP THR PRO PHE SEQRES 5 A 297 GLY LYS PRO SER ASP ALA LEU ILE LEU GLY LYS ILE LYS SEQRES 6 A 297 ASN VAL ASP CYS VAL LEU LEU ALA ARG HIS GLY ARG GLN SEQRES 7 A 297 HIS THR ILE MET PRO SER LYS VAL ASN TYR GLN ALA ASN SEQRES 8 A 297 ILE TRP ALA LEU LYS GLU GLU GLY CYS THR HIS VAL ILE SEQRES 9 A 297 VAL THR THR ALA CYS GLY SER LEU ARG GLU GLU ILE GLN SEQRES 10 A 297 PRO GLY ASP ILE VAL ILE ILE ASP GLN PHE ILE ASP ARG SEQRES 11 A 297 THR THR MET ARG PRO GLN SER PHE TYR ASP GLY SER HIS SEQRES 12 A 297 SER CYS ALA ARG GLY VAL CYS HIS ILE PRO MET ALA GLU SEQRES 13 A 297 PRO PHE CYS PRO LYS THR ARG GLU VAL LEU ILE GLU THR SEQRES 14 A 297 ALA LYS LYS LEU GLY LEU ARG CYS HIS SER LYS GLY THR SEQRES 15 A 297 MET VAL THR ILE GLU GLY PRO ARG PHE SER SER ARG ALA SEQRES 16 A 297 GLU SER PHE MET PHE ARG THR TRP GLY ALA ASP VAL ILE SEQRES 17 A 297 ASN MET THR THR VAL PRO GLU VAL VAL LEU ALA LYS GLU SEQRES 18 A 297 ALA GLY ILE CYS TYR ALA SER ILE ALA MET ALA THR ASP SEQRES 19 A 297 TYR ASP CYS TRP LYS GLU HIS GLU GLU ALA VAL SER VAL SEQRES 20 A 297 ASP ARG VAL LEU LYS THR LEU LYS GLU ASN ALA ASN LYS SEQRES 21 A 297 ALA LYS SER LEU LEU LEU THR THR ILE PRO GLN ILE GLY SEQRES 22 A 297 SER THR GLU TRP SER GLU THR LEU HIS ASN LEU LYS ASN SEQRES 23 A 297 MET ALA GLN PHE SER VAL LEU LEU PRO ARG HIS HET CL A 301 1 HET CL A 302 1 HET PO4 A 303 5 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET OS2 A 307 22 HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM OS2 (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL) HETNAM 2 OS2 METHYL]-4-{[(PROP-2-YN-1-YL) HETNAM 3 OS2 SULFANYL]METHYL}PYRROLIDIN-3-OL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CL 2(CL 1-) FORMUL 4 PO4 O4 P 3- FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 OS2 C15 H19 N5 O S FORMUL 9 HOH *265(H2 O) HELIX 1 AA1 ASP A 22 LEU A 26 5 5 HELIX 2 AA2 MET A 68 VAL A 72 5 5 HELIX 3 AA3 ASN A 73 GLU A 84 1 12 HELIX 4 AA4 CYS A 145 LEU A 159 1 15 HELIX 5 AA5 SER A 179 TRP A 189 1 11 HELIX 6 AA6 THR A 197 ALA A 208 1 12 HELIX 7 AA7 SER A 232 SER A 260 1 29 HELIX 8 AA8 TRP A 263 SER A 277 1 15 SHEET 1 AA1 8 GLU A 27 LYS A 32 0 SHEET 2 AA1 8 LEU A 45 ILE A 50 -1 O LEU A 47 N THR A 30 SHEET 3 AA1 8 VAL A 53 ALA A 59 -1 O LEU A 57 N ILE A 46 SHEET 4 AA1 8 LYS A 11 GLY A 16 1 N ILE A 14 O VAL A 56 SHEET 5 AA1 8 HIS A 88 SER A 97 1 O HIS A 88 N GLY A 13 SHEET 6 AA1 8 VAL A 193 ASN A 195 -1 O ILE A 194 N GLY A 96 SHEET 7 AA1 8 THR A 168 ILE A 172 1 N ILE A 172 O ASN A 195 SHEET 8 AA1 8 GLN A 112 ARG A 116 1 N GLN A 112 O MET A 169 SHEET 1 AA2 8 GLU A 27 LYS A 32 0 SHEET 2 AA2 8 LEU A 45 ILE A 50 -1 O LEU A 47 N THR A 30 SHEET 3 AA2 8 VAL A 53 ALA A 59 -1 O LEU A 57 N ILE A 46 SHEET 4 AA2 8 LYS A 11 GLY A 16 1 N ILE A 14 O VAL A 56 SHEET 5 AA2 8 HIS A 88 SER A 97 1 O HIS A 88 N GLY A 13 SHEET 6 AA2 8 CYS A 211 ASP A 220 1 O MET A 217 N THR A 93 SHEET 7 AA2 8 ILE A 107 VAL A 108 -1 N VAL A 108 O ALA A 216 SHEET 8 AA2 8 CYS A 163 HIS A 164 1 O HIS A 164 N ILE A 107 SHEET 1 AA3 2 VAL A 135 CYS A 136 0 SHEET 2 AA3 2 VAL A 278 LEU A 279 -1 O LEU A 279 N VAL A 135 CISPEP 1 GLY A 174 PRO A 175 0 -3.08 CISPEP 2 VAL A 199 PRO A 200 0 10.49 SITE 1 AC1 2 ARG A 116 HOH A 495 SITE 1 AC2 9 GLY A 17 THR A 18 ARG A 60 HIS A 61 SITE 2 AC2 9 THR A 93 ALA A 94 THR A 197 OS2 A 307 SITE 3 AC2 9 HOH A 415 SITE 1 AC3 5 ASP A 115 ARG A 116 THR A 117 HOH A 473 SITE 2 AC3 5 HOH A 495 SITE 1 AC4 4 LEU A 161 ARG A 162 CYS A 163 HOH A 620 SITE 1 AC5 5 LYS A 40 GLU A 101 LYS A 166 ASP A 192 SITE 2 AC5 5 HOH A 437 SITE 1 AC6 18 THR A 18 HIS A 65 PRO A 69 ALA A 94 SITE 2 AC6 18 CYS A 95 GLY A 96 HIS A 137 PHE A 177 SITE 3 AC6 18 ILE A 194 ASN A 195 MET A 196 THR A 219 SITE 4 AC6 18 ASP A 220 ASP A 222 LEU A 279 PO4 A 303 SITE 5 AC6 18 HOH A 425 HOH A 480 CRYST1 122.821 122.821 44.624 90.00 90.00 120.00 P 3 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 0.008142 0.004701 0.000000 0.00000 SCALE2 0.000000 0.009401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022409 0.00000