HEADER TRANSFERASE/TRANSFERASE INHIBITOR 19-AUG-11 3THS TITLE CRYSTAL STRUCTURE OF RAT NATIVE LIVER GLYCINE N-METHYLTRANSFERASE TITLE 2 COMPLEXED WITH 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINE N-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: FOLATE-BINDING PROTEIN; COMPND 5 EC: 2.1.1.20; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE; COMPND 8 CHAIN: E, F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS GLYCINE N-METHYLTRANSFERASE, GNMT, FOLATE, FOLATE BINDING, KEYWDS 2 TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.LUKA,S.PAKHOMOVA,L.V.LOUKACHEVITCH,M.E.NEWCOMER,C.WAGNER REVDAT 3 13-SEP-23 3THS 1 REMARK SEQADV LINK REVDAT 2 11-JAN-12 3THS 1 JRNL REVDAT 1 16-NOV-11 3THS 0 JRNL AUTH Z.LUKA,S.PAKHOMOVA,L.V.LOUKACHEVITCH,M.E.NEWCOMER,C.WAGNER JRNL TITL DIFFERENCES IN FOLATE-PROTEIN INTERACTIONS RESULT IN JRNL TITL 2 DIFFERING INHIBITION OF NATIVE RAT LIVER AND RECOMBINANT JRNL TITL 3 GLYCINE N-METHYLTRANSFERASE BY 5-METHYLTETRAHYDROFOLATE. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1824 286 2011 JRNL REFN ISSN 0006-3002 JRNL PMID 22037183 JRNL DOI 10.1016/J.BBAPAP.2011.10.008 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 43978 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8984 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.45000 REMARK 3 B22 (A**2) : 4.35000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.324 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.267 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.305 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3THS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-09 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 : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46441 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 34.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56500 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2IDK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M NA-FLUORIDE OR CA REMARK 280 -ACETATE, 100 MM TRIS-HCL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 96.51800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.52350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.51800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.52350 REMARK 290 SMTRY3 4 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE IS PEPTIDE-LIKE, A REMARK 400 MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE REMARK 400 CHAIN: E, F REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 PRO A 225 REMARK 465 GLY A 226 REMARK 465 ALA A 227 REMARK 465 GLY A 228 REMARK 465 ARG A 229 REMARK 465 ASP A 230 REMARK 465 GLY A 231 REMARK 465 ALA A 232 REMARK 465 PRO A 233 REMARK 465 GLY B 226 REMARK 465 ALA B 227 REMARK 465 GLY B 228 REMARK 465 ARG B 229 REMARK 465 ASP B 230 REMARK 465 GLY B 231 REMARK 465 ALA B 232 REMARK 465 PRO C 225 REMARK 465 GLY C 226 REMARK 465 ALA C 227 REMARK 465 GLY C 228 REMARK 465 ARG C 229 REMARK 465 ASP C 230 REMARK 465 GLY C 231 REMARK 465 ALA C 232 REMARK 465 PRO D 225 REMARK 465 GLY D 226 REMARK 465 ALA D 227 REMARK 465 GLY D 228 REMARK 465 ARG D 229 REMARK 465 ASP D 230 REMARK 465 GLY D 231 REMARK 465 ALA D 232 REMARK 465 PRO D 233 REMARK 465 GGL E 4 REMARK 465 GGL E 5 REMARK 465 GGL E 6 REMARK 465 GGL F 4 REMARK 465 GGL F 5 REMARK 465 GGL F 6 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 200 CG CD CE NZ REMARK 470 GLN A 223 CG CD OE1 NE2 REMARK 470 GLN B 223 CG CD OE1 NE2 REMARK 470 LYS C 89 CG CD CE NZ REMARK 470 PHE C 107 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN C 223 CG CD OE1 NE2 REMARK 470 VAL C 224 CG1 CG2 REMARK 470 LYS D 109 CG CD CE NZ REMARK 470 ASP D 197 CG OD1 OD2 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 NZ LYS D 200 CG1 VAL D 222 2.02 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 PRO A 275 NH1 ARG C 154 2556 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 65 CB CYS A 65 SG -0.104 REMARK 500 GLU B 43 CG GLU B 43 CD 0.092 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 THR A 37 16.39 -141.27 REMARK 500 HIS A 58 -54.44 -121.53 REMARK 500 ALA A 64 55.06 -141.25 REMARK 500 GLN A 150 13.52 58.86 REMARK 500 GLN A 277 159.13 -49.59 REMARK 500 ALA B 115 145.39 -170.06 REMARK 500 PHE B 270 -17.24 80.95 REMARK 500 ALA C 115 143.12 -170.97 REMARK 500 GLN C 150 20.00 54.42 REMARK 500 GLN C 223 -150.43 -104.31 REMARK 500 PHE C 235 56.23 -159.42 REMARK 500 PHE C 270 -20.18 82.48 REMARK 500 THR D 37 15.88 -141.29 REMARK 500 HIS D 58 -50.99 -122.91 REMARK 500 GLN D 150 17.08 57.33 REMARK 500 MET D 215 142.02 -170.42 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 BME B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAM B 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN E OF 5 REMARK 800 -METHYLTETRAHYDROFOLATE PENTAGLUTAMATE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF 5 REMARK 800 -METHYLTETRAHYDROFOLATE PENTAGLUTAMATE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3THR RELATED DB: PDB REMARK 900 RELATED ID: 2IDK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH REMARK 900 FOLATE DBREF 3THS A 1 292 UNP P13255 GNMT_RAT 2 293 DBREF 3THS B 1 292 UNP P13255 GNMT_RAT 2 293 DBREF 3THS C 1 292 UNP P13255 GNMT_RAT 2 293 DBREF 3THS D 1 292 UNP P13255 GNMT_RAT 2 293 DBREF 3THS E 1 5 PDB 3THS 3THS 1 5 DBREF 3THS F 1 5 PDB 3THS 3THS 1 5 SEQADV 3THS ACE A 300 UNP P13255 ACETYLATION SEQADV 3THS ACE B 300 UNP P13255 ACETYLATION SEQADV 3THS ACE C 300 UNP P13255 ACETYLATION SEQADV 3THS ACE D 300 UNP P13255 ACETYLATION SEQRES 1 A 293 ACE VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL SEQRES 2 A 293 ALA ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU SEQRES 3 A 293 ALA ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SEQRES 4 A 293 SER ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU SEQRES 5 A 293 LEU ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA SEQRES 6 A 293 CYS GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU SEQRES 7 A 293 GLY PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET SEQRES 8 A 293 LEU LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS SEQRES 9 A 293 GLU PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN SEQRES 10 A 293 TRP LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY SEQRES 11 A 293 PHE ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS SEQRES 12 A 293 LEU PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU SEQRES 13 A 293 ALA LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY SEQRES 14 A 293 LEU LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SEQRES 15 A 293 SER THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR SEQRES 16 A 293 LYS SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU SEQRES 17 A 293 THR VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR SEQRES 18 A 293 THR VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO SEQRES 19 A 293 GLY PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS SEQRES 20 A 293 LEU ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY SEQRES 21 A 293 GLY ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO SEQRES 22 A 293 TYR ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE SEQRES 23 A 293 HIS VAL LEU LYS LYS THR GLY SEQRES 1 B 293 ACE VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL SEQRES 2 B 293 ALA ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU SEQRES 3 B 293 ALA ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SEQRES 4 B 293 SER ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU SEQRES 5 B 293 LEU ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA SEQRES 6 B 293 CYS GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU SEQRES 7 B 293 GLY PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET SEQRES 8 B 293 LEU LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS SEQRES 9 B 293 GLU PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN SEQRES 10 B 293 TRP LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY SEQRES 11 B 293 PHE ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS SEQRES 12 B 293 LEU PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU SEQRES 13 B 293 ALA LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY SEQRES 14 B 293 LEU LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SEQRES 15 B 293 SER THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR SEQRES 16 B 293 LYS SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU SEQRES 17 B 293 THR VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR SEQRES 18 B 293 THR VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO SEQRES 19 B 293 GLY PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS SEQRES 20 B 293 LEU ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY SEQRES 21 B 293 GLY ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO SEQRES 22 B 293 TYR ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE SEQRES 23 B 293 HIS VAL LEU LYS LYS THR GLY SEQRES 1 C 293 ACE VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL SEQRES 2 C 293 ALA ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU SEQRES 3 C 293 ALA ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SEQRES 4 C 293 SER ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU SEQRES 5 C 293 LEU ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA SEQRES 6 C 293 CYS GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU SEQRES 7 C 293 GLY PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET SEQRES 8 C 293 LEU LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS SEQRES 9 C 293 GLU PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN SEQRES 10 C 293 TRP LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY SEQRES 11 C 293 PHE ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS SEQRES 12 C 293 LEU PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU SEQRES 13 C 293 ALA LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY SEQRES 14 C 293 LEU LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SEQRES 15 C 293 SER THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR SEQRES 16 C 293 LYS SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU SEQRES 17 C 293 THR VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR SEQRES 18 C 293 THR VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO SEQRES 19 C 293 GLY PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS SEQRES 20 C 293 LEU ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY SEQRES 21 C 293 GLY ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO SEQRES 22 C 293 TYR ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE SEQRES 23 C 293 HIS VAL LEU LYS LYS THR GLY SEQRES 1 D 293 ACE VAL ASP SER VAL TYR ARG THR ARG SER LEU GLY VAL SEQRES 2 D 293 ALA ALA GLU GLY ILE PRO ASP GLN TYR ALA ASP GLY GLU SEQRES 3 D 293 ALA ALA ARG VAL TRP GLN LEU TYR ILE GLY ASP THR ARG SEQRES 4 D 293 SER ARG THR ALA GLU TYR LYS ALA TRP LEU LEU GLY LEU SEQRES 5 D 293 LEU ARG GLN HIS GLY CYS HIS ARG VAL LEU ASP VAL ALA SEQRES 6 D 293 CYS GLY THR GLY VAL ASP SER ILE MET LEU VAL GLU GLU SEQRES 7 D 293 GLY PHE SER VAL THR SER VAL ASP ALA SER ASP LYS MET SEQRES 8 D 293 LEU LYS TYR ALA LEU LYS GLU ARG TRP ASN ARG ARG LYS SEQRES 9 D 293 GLU PRO ALA PHE ASP LYS TRP VAL ILE GLU GLU ALA ASN SEQRES 10 D 293 TRP LEU THR LEU ASP LYS ASP VAL PRO ALA GLY ASP GLY SEQRES 11 D 293 PHE ASP ALA VAL ILE CYS LEU GLY ASN SER PHE ALA HIS SEQRES 12 D 293 LEU PRO ASP SER LYS GLY ASP GLN SER GLU HIS ARG LEU SEQRES 13 D 293 ALA LEU LYS ASN ILE ALA SER MET VAL ARG PRO GLY GLY SEQRES 14 D 293 LEU LEU VAL ILE ASP HIS ARG ASN TYR ASP TYR ILE LEU SEQRES 15 D 293 SER THR GLY CYS ALA PRO PRO GLY LYS ASN ILE TYR TYR SEQRES 16 D 293 LYS SER ASP LEU THR LYS ASP ILE THR THR SER VAL LEU SEQRES 17 D 293 THR VAL ASN ASN LYS ALA HIS MET VAL THR LEU ASP TYR SEQRES 18 D 293 THR VAL GLN VAL PRO GLY ALA GLY ARG ASP GLY ALA PRO SEQRES 19 D 293 GLY PHE SER LYS PHE ARG LEU SER TYR TYR PRO HIS CYS SEQRES 20 D 293 LEU ALA SER PHE THR GLU LEU VAL GLN GLU ALA PHE GLY SEQRES 21 D 293 GLY ARG CYS GLN HIS SER VAL LEU GLY ASP PHE LYS PRO SEQRES 22 D 293 TYR ARG PRO GLY GLN ALA TYR VAL PRO CYS TYR PHE ILE SEQRES 23 D 293 HIS VAL LEU LYS LYS THR GLY SEQRES 1 E 6 03O GGL GGL GGL GGL GGL SEQRES 1 F 6 03O GGL GGL GGL GGL GGL HET ACE A 300 3 HET ACE B 300 3 HET ACE C 300 3 HET ACE D 300 3 HET 03O E 1 23 HET GGL E 2 9 HET GGL E 3 1 HET 03O F 1 23 HET GGL F 2 9 HET GGL F 3 1 HET BME B 400 8 HET TAM B 293 11 HETNAM ACE ACETYL GROUP HETNAM 03O 4-({[(6S)-2-AMINO-5-METHYL-4-OXO-3,4,5,6,7,8- HETNAM 2 03O HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOIC ACID HETNAM GGL GAMMA-L-GLUTAMIC ACID HETNAM BME BETA-MERCAPTOETHANOL HETNAM TAM TRIS(HYDROXYETHYL)AMINOMETHANE HETSYN 03O 5-METHYL TETRAHYDROPTEROIC ACID HETSYN GGL L-GLUTAMIC ACID FORMUL 1 ACE 4(C2 H4 O) FORMUL 5 03O 2(C15 H18 N6 O3) FORMUL 5 GGL 4(C5 H9 N O4) FORMUL 7 BME C2 H6 O S FORMUL 8 TAM C7 H17 N O3 FORMUL 9 HOH *88(H2 O) HELIX 1 1 GLY A 24 GLY A 35 1 12 HELIX 2 2 THR A 41 HIS A 55 1 15 HELIX 3 3 GLY A 68 GLU A 77 1 10 HELIX 4 4 SER A 87 ARG A 101 1 15 HELIX 5 5 GLU A 104 LYS A 109 1 6 HELIX 6 6 ASN A 116 LEU A 118 5 3 HELIX 7 7 THR A 119 VAL A 124 1 6 HELIX 8 8 SER A 139 LEU A 143 5 5 HELIX 9 9 GLN A 150 SER A 162 1 13 HELIX 10 10 ASN A 176 GLY A 184 1 9 HELIX 11 11 CYS A 246 PHE A 258 1 13 HELIX 12 12 GLY B 24 ASP B 36 1 13 HELIX 13 13 THR B 41 HIS B 55 1 15 HELIX 14 14 GLY B 68 GLU B 77 1 10 HELIX 15 15 SER B 87 ARG B 101 1 15 HELIX 16 16 GLU B 104 LYS B 109 1 6 HELIX 17 17 ASN B 116 LEU B 118 5 3 HELIX 18 18 THR B 119 VAL B 124 1 6 HELIX 19 19 SER B 139 LEU B 143 5 5 HELIX 20 20 GLN B 150 SER B 162 1 13 HELIX 21 21 ASN B 176 GLY B 184 1 9 HELIX 22 22 CYS B 246 ALA B 257 1 12 HELIX 23 23 GLY C 24 ASP C 36 1 13 HELIX 24 24 THR C 41 HIS C 55 1 15 HELIX 25 25 GLY C 68 GLU C 77 1 10 HELIX 26 26 SER C 87 ARG C 101 1 15 HELIX 27 27 GLU C 104 LYS C 109 1 6 HELIX 28 28 ASN C 116 LEU C 118 5 3 HELIX 29 29 THR C 119 VAL C 124 1 6 HELIX 30 30 ASN C 138 LEU C 143 5 6 HELIX 31 31 GLN C 150 SER C 162 1 13 HELIX 32 32 ASN C 176 GLY C 184 1 9 HELIX 33 33 CYS C 246 PHE C 258 1 13 HELIX 34 34 GLY D 24 ASP D 36 1 13 HELIX 35 35 THR D 41 HIS D 55 1 15 HELIX 36 36 GLY D 68 GLY D 78 1 11 HELIX 37 37 SER D 87 ARG D 101 1 15 HELIX 38 38 GLU D 104 LYS D 109 1 6 HELIX 39 39 ASN D 116 LEU D 118 5 3 HELIX 40 40 THR D 119 VAL D 124 1 6 HELIX 41 41 SER D 139 LEU D 143 5 5 HELIX 42 42 GLN D 150 SER D 162 1 13 HELIX 43 43 ASN D 176 GLY D 184 1 9 HELIX 44 44 CYS D 246 PHE D 258 1 13 SHEET 1 A 2 VAL A 4 ARG A 6 0 SHEET 2 A 2 VAL C 4 ARG C 6 -1 O TYR C 5 N TYR A 5 SHEET 1 B 8 VAL A 111 GLU A 114 0 SHEET 2 B 8 SER A 80 ASP A 85 1 N SER A 83 O VAL A 111 SHEET 3 B 8 ARG A 59 ASP A 62 1 N ASP A 62 O THR A 82 SHEET 4 B 8 PHE A 130 CYS A 135 1 O ILE A 134 N LEU A 61 SHEET 5 B 8 VAL A 164 ARG A 175 1 O VAL A 171 N VAL A 133 SHEET 6 B 8 TYR A 283 LYS A 290 -1 O HIS A 286 N ILE A 172 SHEET 7 B 8 CYS A 262 GLY A 268 -1 N LEU A 267 O ILE A 285 SHEET 8 B 8 LYS A 271 PRO A 272 -1 O LYS A 271 N GLY A 268 SHEET 1 C 6 SER A 236 TYR A 242 0 SHEET 2 C 6 LYS A 212 VAL A 222 -1 N TYR A 220 O PHE A 238 SHEET 3 C 6 ASP A 201 VAL A 209 -1 N SER A 205 O THR A 217 SHEET 4 C 6 ASP C 201 VAL C 209 -1 O THR C 208 N VAL A 206 SHEET 5 C 6 LYS C 212 VAL C 222 -1 O THR C 217 N SER C 205 SHEET 6 C 6 SER C 236 TYR C 242 -1 O SER C 236 N VAL C 222 SHEET 1 D 2 VAL B 4 ARG B 6 0 SHEET 2 D 2 VAL D 4 ARG D 6 -1 O TYR D 5 N TYR B 5 SHEET 1 E 8 VAL B 111 GLU B 114 0 SHEET 2 E 8 SER B 80 ASP B 85 1 N SER B 83 O VAL B 111 SHEET 3 E 8 ARG B 59 ASP B 62 1 N ASP B 62 O VAL B 84 SHEET 4 E 8 PHE B 130 CYS B 135 1 O ILE B 134 N LEU B 61 SHEET 5 E 8 VAL B 164 ARG B 175 1 O ARG B 165 N PHE B 130 SHEET 6 E 8 TYR B 283 LYS B 290 -1 O LEU B 288 N LEU B 170 SHEET 7 E 8 CYS B 262 GLY B 268 -1 N SER B 265 O VAL B 287 SHEET 8 E 8 LYS B 271 PRO B 272 -1 O LYS B 271 N GLY B 268 SHEET 1 F 6 GLY B 234 TYR B 242 0 SHEET 2 F 6 LYS B 212 VAL B 224 -1 N TYR B 220 O PHE B 238 SHEET 3 F 6 LYS B 200 VAL B 209 -1 N SER B 205 O THR B 217 SHEET 4 F 6 ASP D 201 VAL D 209 -1 O VAL D 206 N THR B 208 SHEET 5 F 6 LYS D 212 VAL D 222 -1 O THR D 217 N SER D 205 SHEET 6 F 6 SER D 236 TYR D 242 -1 O PHE D 238 N TYR D 220 SHEET 1 G 8 VAL C 111 GLU C 114 0 SHEET 2 G 8 SER C 80 ASP C 85 1 N SER C 83 O VAL C 111 SHEET 3 G 8 ARG C 59 ASP C 62 1 N VAL C 60 O SER C 80 SHEET 4 G 8 PHE C 130 CYS C 135 1 O ILE C 134 N LEU C 61 SHEET 5 G 8 VAL C 164 ARG C 175 1 O ARG C 165 N PHE C 130 SHEET 6 G 8 TYR C 283 LYS C 290 -1 O HIS C 286 N ILE C 172 SHEET 7 G 8 CYS C 262 GLY C 268 -1 N SER C 265 O VAL C 287 SHEET 8 G 8 LYS C 271 PRO C 272 -1 O LYS C 271 N GLY C 268 SHEET 1 H 8 VAL D 111 GLU D 114 0 SHEET 2 H 8 SER D 80 ASP D 85 1 N SER D 83 O VAL D 111 SHEET 3 H 8 ARG D 59 ASP D 62 1 N ASP D 62 O THR D 82 SHEET 4 H 8 PHE D 130 CYS D 135 1 O ALA D 132 N LEU D 61 SHEET 5 H 8 VAL D 164 ARG D 175 1 O LEU D 169 N ASP D 131 SHEET 6 H 8 TYR D 283 LYS D 290 -1 O HIS D 286 N ILE D 172 SHEET 7 H 8 CYS D 262 GLY D 268 -1 N LEU D 267 O ILE D 285 SHEET 8 H 8 LYS D 271 PRO D 272 -1 O LYS D 271 N GLY D 268 LINK N VAL A 1 C ACE A 300 1555 1555 1.36 LINK N VAL B 1 C ACE B 300 1555 1555 1.34 LINK SG CYS B 185 S2 ABME B 400 1555 1555 2.08 LINK SG CYS B 185 S2 BBME B 400 1555 1555 2.05 LINK N VAL C 1 C ACE C 300 1555 1555 1.34 LINK N VAL D 1 C ACE D 300 1555 1555 1.35 LINK C 03O E 1 N GGL E 2 1555 1555 1.33 LINK CD GGL E 2 N GGL E 3 1555 1555 1.34 LINK C 03O F 1 N GGL F 2 1555 1555 1.32 LINK CD GGL F 2 N GGL F 3 1555 1555 1.34 SITE 1 AC1 7 CYS B 185 ILE B 202 THR B 203 THR B 204 SITE 2 AC1 7 ASN D 210 GLY D 276 ALA D 278 SITE 1 AC2 7 GLU A 15 TYR B 33 ILE B 34 GLY B 137 SITE 2 AC2 7 HIS B 142 ASN B 191 TYR B 242 SITE 1 AC3 12 TYR A 5 THR A 7 SER B 205 LEU B 207 SITE 2 AC3 12 THR B 217 ARG B 239 SER C 3 VAL C 4 SITE 3 AC3 12 TYR C 5 LEU D 207 HIS D 214 MET D 215 SITE 1 AC4 12 LEU A 207 HIS A 214 MET A 215 SER B 3 SITE 2 AC4 12 VAL B 4 TYR B 5 SER C 146 HIS C 214 SITE 3 AC4 12 MET C 215 ARG C 239 TYR D 5 ARG D 6 CRYST1 193.036 61.047 146.352 90.00 128.92 90.00 C 1 2 1 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 0.005180 0.000000 0.004183 0.00000 SCALE2 0.000000 0.016381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008782 0.00000 HETATM 1 C ACE A 300 -15.614 40.267 20.517 1.00 50.03 C HETATM 2 O ACE A 300 -15.215 39.052 20.502 1.00 50.10 O HETATM 3 CH3 ACE A 300 -16.656 40.817 19.583 1.00 48.69 C