HEADER TRANSFERASE 03-MAR-19 6QVL TITLE HUMAN SHMT2 IN COMPLEX WITH PEMETREXED COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHMT,GLYCINE HYDROXYMETHYLTRANSFERASE,SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; 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: SHMT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SCALETTI,A.S.JEMTH,T.HELLEDAY,P.STENMARK REVDAT 1 04-SEP-19 6QVL 0 JRNL AUTH E.SCALETTI,A.S.JEMTH,T.HELLEDAY,P.STENMARK JRNL TITL STRUCTURAL BASIS OF INHIBITION OF THE HUMAN SERINE JRNL TITL 2 HYDROXYMETHYLTRANSFERASE SHMT2 BY ANTIFOLATE DRUGS. JRNL REF FEBS LETT. V. 593 1863 2019 JRNL REFN ISSN 0014-5793 JRNL PMID 31127856 JRNL DOI 10.1002/1873-3468.13455 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 69006 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3602 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4999 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7087 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : -3.19000 REMARK 3 B12 (A**2) : 0.49000 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): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.342 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7357 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6892 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9951 ; 1.396 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15925 ; 0.950 ; 2.997 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 911 ; 6.583 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 343 ;35.370 ;22.770 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1236 ;15.699 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 72 ;15.890 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1087 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8237 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1558 ; 0.001 ; 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): 3644 ; 2.002 ; 3.986 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3643 ; 2.002 ; 3.986 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4555 ; 3.334 ; 5.968 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4556 ; 3.334 ; 5.968 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3712 ; 1.898 ; 4.256 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3713 ; 1.898 ; 4.257 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5397 ; 3.300 ; 6.269 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8319 ; 6.266 ;47.058 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8320 ; 6.265 ;47.058 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 6QVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292100975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1458540 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 52.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 52.70 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LICL2, 0.1 M MES PH 6.0, 20 % REMARK 280 PEG6000, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 139.62800 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 69.81400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 104.72100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.90700 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 174.53500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 139.62800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 69.81400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.90700 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.72100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 174.53500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 LEU A 2 REMARK 465 TYR A 3 REMARK 465 PHE A 4 REMARK 465 SER A 5 REMARK 465 LEU A 6 REMARK 465 PHE A 7 REMARK 465 TRP A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 ARG A 11 REMARK 465 PRO A 12 REMARK 465 LEU A 13 REMARK 465 GLN A 14 REMARK 465 ARG A 15 REMARK 465 CYS A 16 REMARK 465 GLY A 17 REMARK 465 GLN A 18 REMARK 465 LEU A 19 REMARK 465 VAL A 20 REMARK 465 ARG A 21 REMARK 465 MET A 22 REMARK 465 ALA A 23 REMARK 465 ILE A 24 REMARK 465 ARG A 25 REMARK 465 ALA A 26 REMARK 465 GLN A 27 REMARK 465 HIS A 28 REMARK 465 SER A 29 REMARK 465 ASN A 30 REMARK 465 ALA A 31 REMARK 465 ALA A 32 REMARK 465 GLN A 33 REMARK 465 THR A 34 REMARK 465 GLN A 35 REMARK 465 THR A 36 REMARK 465 GLY A 37 REMARK 465 GLU A 38 REMARK 465 ALA A 39 REMARK 465 ASN A 40 REMARK 465 ARG A 41 REMARK 465 GLY A 42 REMARK 465 ALA A 298 REMARK 465 VAL A 299 REMARK 465 ASP A 300 REMARK 465 PRO A 301 REMARK 465 LYS A 302 REMARK 465 THR A 303 REMARK 465 GLY A 304 REMARK 465 ARG A 305 REMARK 465 GLU A 306 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 TYR B 3 REMARK 465 PHE B 4 REMARK 465 SER B 5 REMARK 465 LEU B 6 REMARK 465 PHE B 7 REMARK 465 TRP B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 ARG B 11 REMARK 465 PRO B 12 REMARK 465 LEU B 13 REMARK 465 GLN B 14 REMARK 465 ARG B 15 REMARK 465 CYS B 16 REMARK 465 GLY B 17 REMARK 465 GLN B 18 REMARK 465 LEU B 19 REMARK 465 VAL B 20 REMARK 465 ARG B 21 REMARK 465 MET B 22 REMARK 465 ALA B 23 REMARK 465 ILE B 24 REMARK 465 ARG B 25 REMARK 465 ALA B 26 REMARK 465 GLN B 27 REMARK 465 HIS B 28 REMARK 465 SER B 29 REMARK 465 ASN B 30 REMARK 465 ALA B 31 REMARK 465 ALA B 32 REMARK 465 GLN B 33 REMARK 465 THR B 34 REMARK 465 GLN B 35 REMARK 465 THR B 36 REMARK 465 GLY B 37 REMARK 465 GLU B 38 REMARK 465 ALA B 39 REMARK 465 ASN B 40 REMARK 465 ARG B 41 REMARK 465 GLY B 42 REMARK 465 VAL B 299 REMARK 465 ASP B 300 REMARK 465 PRO B 301 REMARK 465 LYS B 302 REMARK 465 THR B 303 REMARK 465 GLY B 304 REMARK 465 ARG B 305 REMARK 465 GLU B 306 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 SER A 97 49.07 -142.51 REMARK 500 LYS A 103 50.90 -152.00 REMARK 500 HIS A 279 -158.71 -74.82 REMARK 500 LYS A 280 -137.25 63.32 REMARK 500 SER A 287 -176.47 -171.36 REMARK 500 ASN A 379 -145.35 -137.19 REMARK 500 ALA A 418 -52.80 176.74 REMARK 500 ALA A 463 -71.32 -99.03 REMARK 500 SER B 142 -169.61 -163.63 REMARK 500 ASP B 205 88.79 -69.49 REMARK 500 ALA B 227 71.81 -151.41 REMARK 500 HIS B 279 -157.35 -88.83 REMARK 500 LYS B 280 -126.46 63.73 REMARK 500 SER B 287 -165.37 -168.35 REMARK 500 LYS B 297 -65.05 -91.30 REMARK 500 ASN B 379 -155.20 -150.75 REMARK 500 LEU B 391 -152.75 -138.70 REMARK 500 ALA B 463 -79.84 -97.31 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 GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4DW B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 603 and LYS B REMARK 800 280 DBREF 6QVL A 1 504 UNP P34897 GLYM_HUMAN 1 504 DBREF 6QVL B 1 504 UNP P34897 GLYM_HUMAN 1 504 SEQRES 1 A 504 MET LEU TYR PHE SER LEU PHE TRP ALA ALA ARG PRO LEU SEQRES 2 A 504 GLN ARG CYS GLY GLN LEU VAL ARG MET ALA ILE ARG ALA SEQRES 3 A 504 GLN HIS SER ASN ALA ALA GLN THR GLN THR GLY GLU ALA SEQRES 4 A 504 ASN ARG GLY TRP THR GLY GLN GLU SER LEU SER ASP SER SEQRES 5 A 504 ASP PRO GLU MET TRP GLU LEU LEU GLN ARG GLU LYS ASP SEQRES 6 A 504 ARG GLN CYS ARG GLY LEU GLU LEU ILE ALA SER GLU ASN SEQRES 7 A 504 PHE CYS SER ARG ALA ALA LEU GLU ALA LEU GLY SER CYS SEQRES 8 A 504 LEU ASN ASN LYS TYR SER GLU GLY TYR PRO GLY LYS ARG SEQRES 9 A 504 TYR TYR GLY GLY ALA GLU VAL VAL ASP GLU ILE GLU LEU SEQRES 10 A 504 LEU CYS GLN ARG ARG ALA LEU GLU ALA PHE ASP LEU ASP SEQRES 11 A 504 PRO ALA GLN TRP GLY VAL ASN VAL GLN PRO TYR SER GLY SEQRES 12 A 504 SER PRO ALA ASN LEU ALA VAL TYR THR ALA LEU LEU GLN SEQRES 13 A 504 PRO HIS ASP ARG ILE MET GLY LEU ASP LEU PRO ASP GLY SEQRES 14 A 504 GLY HIS LEU THR HIS GLY TYR MET SER ASP VAL LYS ARG SEQRES 15 A 504 ILE SER ALA THR SER ILE PHE PHE GLU SER MET PRO TYR SEQRES 16 A 504 LYS LEU ASN PRO LYS THR GLY LEU ILE ASP TYR ASN GLN SEQRES 17 A 504 LEU ALA LEU THR ALA ARG LEU PHE ARG PRO ARG LEU ILE SEQRES 18 A 504 ILE ALA GLY THR SER ALA TYR ALA ARG LEU ILE ASP TYR SEQRES 19 A 504 ALA ARG MET ARG GLU VAL CYS ASP GLU VAL LYS ALA HIS SEQRES 20 A 504 LEU LEU ALA ASP MET ALA HIS ILE SER GLY LEU VAL ALA SEQRES 21 A 504 ALA LYS VAL ILE PRO SER PRO PHE LYS HIS ALA ASP ILE SEQRES 22 A 504 VAL THR THR THR THR HIS LYS THR LEU ARG GLY ALA ARG SEQRES 23 A 504 SER GLY LEU ILE PHE TYR ARG LYS GLY VAL LYS ALA VAL SEQRES 24 A 504 ASP PRO LYS THR GLY ARG GLU ILE PRO TYR THR PHE GLU SEQRES 25 A 504 ASP ARG ILE ASN PHE ALA VAL PHE PRO SER LEU GLN GLY SEQRES 26 A 504 GLY PRO HIS ASN HIS ALA ILE ALA ALA VAL ALA VAL ALA SEQRES 27 A 504 LEU LYS GLN ALA CYS THR PRO MET PHE ARG GLU TYR SER SEQRES 28 A 504 LEU GLN VAL LEU LYS ASN ALA ARG ALA MET ALA ASP ALA SEQRES 29 A 504 LEU LEU GLU ARG GLY TYR SER LEU VAL SER GLY GLY THR SEQRES 30 A 504 ASP ASN HIS LEU VAL LEU VAL ASP LEU ARG PRO LYS GLY SEQRES 31 A 504 LEU ASP GLY ALA ARG ALA GLU ARG VAL LEU GLU LEU VAL SEQRES 32 A 504 SER ILE THR ALA ASN LYS ASN THR CYS PRO GLY ASP ARG SEQRES 33 A 504 SER ALA ILE THR PRO GLY GLY LEU ARG LEU GLY ALA PRO SEQRES 34 A 504 ALA LEU THR SER ARG GLN PHE ARG GLU ASP ASP PHE ARG SEQRES 35 A 504 ARG VAL VAL ASP PHE ILE ASP GLU GLY VAL ASN ILE GLY SEQRES 36 A 504 LEU GLU VAL LYS SER LYS THR ALA LYS LEU GLN ASP PHE SEQRES 37 A 504 LYS SER PHE LEU LEU LYS ASP SER GLU THR SER GLN ARG SEQRES 38 A 504 LEU ALA ASN LEU ARG GLN ARG VAL GLU GLN PHE ALA ARG SEQRES 39 A 504 ALA PHE PRO MET PRO GLY PHE ASP GLU HIS SEQRES 1 B 504 MET LEU TYR PHE SER LEU PHE TRP ALA ALA ARG PRO LEU SEQRES 2 B 504 GLN ARG CYS GLY GLN LEU VAL ARG MET ALA ILE ARG ALA SEQRES 3 B 504 GLN HIS SER ASN ALA ALA GLN THR GLN THR GLY GLU ALA SEQRES 4 B 504 ASN ARG GLY TRP THR GLY GLN GLU SER LEU SER ASP SER SEQRES 5 B 504 ASP PRO GLU MET TRP GLU LEU LEU GLN ARG GLU LYS ASP SEQRES 6 B 504 ARG GLN CYS ARG GLY LEU GLU LEU ILE ALA SER GLU ASN SEQRES 7 B 504 PHE CYS SER ARG ALA ALA LEU GLU ALA LEU GLY SER CYS SEQRES 8 B 504 LEU ASN ASN LYS TYR SER GLU GLY TYR PRO GLY LYS ARG SEQRES 9 B 504 TYR TYR GLY GLY ALA GLU VAL VAL ASP GLU ILE GLU LEU SEQRES 10 B 504 LEU CYS GLN ARG ARG ALA LEU GLU ALA PHE ASP LEU ASP SEQRES 11 B 504 PRO ALA GLN TRP GLY VAL ASN VAL GLN PRO TYR SER GLY SEQRES 12 B 504 SER PRO ALA ASN LEU ALA VAL TYR THR ALA LEU LEU GLN SEQRES 13 B 504 PRO HIS ASP ARG ILE MET GLY LEU ASP LEU PRO ASP GLY SEQRES 14 B 504 GLY HIS LEU THR HIS GLY TYR MET SER ASP VAL LYS ARG SEQRES 15 B 504 ILE SER ALA THR SER ILE PHE PHE GLU SER MET PRO TYR SEQRES 16 B 504 LYS LEU ASN PRO LYS THR GLY LEU ILE ASP TYR ASN GLN SEQRES 17 B 504 LEU ALA LEU THR ALA ARG LEU PHE ARG PRO ARG LEU ILE SEQRES 18 B 504 ILE ALA GLY THR SER ALA TYR ALA ARG LEU ILE ASP TYR SEQRES 19 B 504 ALA ARG MET ARG GLU VAL CYS ASP GLU VAL LYS ALA HIS SEQRES 20 B 504 LEU LEU ALA ASP MET ALA HIS ILE SER GLY LEU VAL ALA SEQRES 21 B 504 ALA LYS VAL ILE PRO SER PRO PHE LYS HIS ALA ASP ILE SEQRES 22 B 504 VAL THR THR THR THR HIS LYS THR LEU ARG GLY ALA ARG SEQRES 23 B 504 SER GLY LEU ILE PHE TYR ARG LYS GLY VAL LYS ALA VAL SEQRES 24 B 504 ASP PRO LYS THR GLY ARG GLU ILE PRO TYR THR PHE GLU SEQRES 25 B 504 ASP ARG ILE ASN PHE ALA VAL PHE PRO SER LEU GLN GLY SEQRES 26 B 504 GLY PRO HIS ASN HIS ALA ILE ALA ALA VAL ALA VAL ALA SEQRES 27 B 504 LEU LYS GLN ALA CYS THR PRO MET PHE ARG GLU TYR SER SEQRES 28 B 504 LEU GLN VAL LEU LYS ASN ALA ARG ALA MET ALA ASP ALA SEQRES 29 B 504 LEU LEU GLU ARG GLY TYR SER LEU VAL SER GLY GLY THR SEQRES 30 B 504 ASP ASN HIS LEU VAL LEU VAL ASP LEU ARG PRO LYS GLY SEQRES 31 B 504 LEU ASP GLY ALA ARG ALA GLU ARG VAL LEU GLU LEU VAL SEQRES 32 B 504 SER ILE THR ALA ASN LYS ASN THR CYS PRO GLY ASP ARG SEQRES 33 B 504 SER ALA ILE THR PRO GLY GLY LEU ARG LEU GLY ALA PRO SEQRES 34 B 504 ALA LEU THR SER ARG GLN PHE ARG GLU ASP ASP PHE ARG SEQRES 35 B 504 ARG VAL VAL ASP PHE ILE ASP GLU GLY VAL ASN ILE GLY SEQRES 36 B 504 LEU GLU VAL LYS SER LYS THR ALA LYS LEU GLN ASP PHE SEQRES 37 B 504 LYS SER PHE LEU LEU LYS ASP SER GLU THR SER GLN ARG SEQRES 38 B 504 LEU ALA ASN LEU ARG GLN ARG VAL GLU GLN PHE ALA ARG SEQRES 39 B 504 ALA PHE PRO MET PRO GLY PHE ASP GLU HIS HET GOL A 601 6 HET GOL A 602 6 HET PEG A 603 7 HET CA A 604 1 HET PLP A 605 15 HET GOL B 601 6 HET 4DW B 602 31 HET PLP B 603 15 HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CA CALCIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM 4DW N-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3- HETNAM 2 4DW D]PYRIMIDIN-5-YL)ETHYL]BENZOYL}-L-GLUTAMIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN 4DW PEMETREXED FORMUL 3 GOL 3(C3 H8 O3) FORMUL 5 PEG C4 H10 O3 FORMUL 6 CA CA 2+ FORMUL 7 PLP 2(C8 H10 N O6 P) FORMUL 9 4DW C20 H19 N5 O6 FORMUL 11 HOH *429(H2 O) HELIX 1 AA1 SER A 48 ASP A 53 1 6 HELIX 2 AA2 ASP A 53 GLY A 70 1 18 HELIX 3 AA3 SER A 81 GLY A 89 1 9 HELIX 4 AA4 SER A 90 LYS A 95 5 6 HELIX 5 AA5 ALA A 109 PHE A 127 1 19 HELIX 6 AA6 SER A 142 LEU A 155 1 14 HELIX 7 AA7 LEU A 166 GLY A 169 5 4 HELIX 8 AA8 HIS A 171 GLY A 175 5 5 HELIX 9 AA9 ALA A 185 PHE A 190 1 6 HELIX 10 AB1 ASP A 205 ARG A 217 1 13 HELIX 11 AB2 ASP A 233 LYS A 245 1 13 HELIX 12 AB3 ILE A 255 ALA A 261 1 7 HELIX 13 AB4 SER A 266 HIS A 270 5 5 HELIX 14 AB5 HIS A 279 ARG A 283 5 5 HELIX 15 AB6 PHE A 311 PHE A 320 1 10 HELIX 16 AB7 HIS A 328 ALA A 342 1 15 HELIX 17 AB8 THR A 344 ARG A 368 1 25 HELIX 18 AB9 SER A 374 GLY A 376 5 3 HELIX 19 AC1 ARG A 387 GLY A 390 5 4 HELIX 20 AC2 ASP A 392 VAL A 403 1 12 HELIX 21 AC3 ALA A 428 ARG A 434 1 7 HELIX 22 AC4 ARG A 437 SER A 460 1 24 HELIX 23 AC5 LYS A 464 ASP A 475 1 12 HELIX 24 AC6 ASP A 475 ALA A 495 1 21 HELIX 25 AC7 SER B 48 ASP B 53 1 6 HELIX 26 AC8 ASP B 53 GLY B 70 1 18 HELIX 27 AC9 SER B 81 GLY B 89 1 9 HELIX 28 AD1 SER B 90 LYS B 95 5 6 HELIX 29 AD2 ALA B 109 PHE B 127 1 19 HELIX 30 AD3 SER B 142 LEU B 155 1 14 HELIX 31 AD4 HIS B 171 GLY B 175 5 5 HELIX 32 AD5 SER B 184 PHE B 190 1 7 HELIX 33 AD6 ASP B 205 ARG B 217 1 13 HELIX 34 AD7 ASP B 233 VAL B 244 1 12 HELIX 35 AD8 ILE B 255 ALA B 261 1 7 HELIX 36 AD9 SER B 266 HIS B 270 5 5 HELIX 37 AE1 HIS B 279 ARG B 283 5 5 HELIX 38 AE2 THR B 310 PHE B 320 1 11 HELIX 39 AE3 HIS B 328 CYS B 343 1 16 HELIX 40 AE4 THR B 344 GLU B 367 1 24 HELIX 41 AE5 ARG B 387 GLY B 390 5 4 HELIX 42 AE6 ASP B 392 VAL B 403 1 12 HELIX 43 AE7 ALA B 428 ARG B 434 1 7 HELIX 44 AE8 ARG B 437 SER B 460 1 24 HELIX 45 AE9 LYS B 464 ASP B 475 1 12 HELIX 46 AF1 ASP B 475 ALA B 495 1 21 SHEET 1 AA1 2 LEU A 71 GLU A 72 0 SHEET 2 AA1 2 ILE A 405 THR A 406 1 O THR A 406 N LEU A 71 SHEET 1 AA2 2 GLY A 99 TYR A 100 0 SHEET 2 AA2 2 LYS A 103 ARG A 104 -1 O LYS A 103 N TYR A 100 SHEET 1 AA3 7 TRP A 134 ASN A 137 0 SHEET 2 AA3 7 GLY A 288 ARG A 293 -1 O ILE A 290 N ASN A 137 SHEET 3 AA3 7 ILE A 273 THR A 277 -1 N VAL A 274 O PHE A 291 SHEET 4 AA3 7 HIS A 247 ASP A 251 1 N ALA A 250 O ILE A 273 SHEET 5 AA3 7 LEU A 220 ALA A 223 1 N ALA A 223 O LEU A 249 SHEET 6 AA3 7 ARG A 160 LEU A 164 1 N MET A 162 O ILE A 222 SHEET 7 AA3 7 GLU A 191 TYR A 195 1 O GLU A 191 N ILE A 161 SHEET 1 AA4 4 SER A 371 LEU A 372 0 SHEET 2 AA4 4 LEU A 381 ASP A 385 -1 O ASP A 385 N SER A 371 SHEET 3 AA4 4 GLY A 423 GLY A 427 -1 O LEU A 424 N VAL A 384 SHEET 4 AA4 4 ASN A 408 ASN A 410 -1 N ASN A 408 O ARG A 425 SHEET 1 AA5 2 LEU B 71 GLU B 72 0 SHEET 2 AA5 2 ILE B 405 THR B 406 1 O THR B 406 N LEU B 71 SHEET 1 AA6 2 GLY B 99 TYR B 100 0 SHEET 2 AA6 2 LYS B 103 ARG B 104 -1 O LYS B 103 N TYR B 100 SHEET 1 AA7 7 TRP B 134 ASN B 137 0 SHEET 2 AA7 7 GLY B 288 ARG B 293 -1 O TYR B 292 N GLY B 135 SHEET 3 AA7 7 ILE B 273 THR B 277 -1 N VAL B 274 O PHE B 291 SHEET 4 AA7 7 HIS B 247 ASP B 251 1 N ALA B 250 O ILE B 273 SHEET 5 AA7 7 LEU B 220 ALA B 223 1 N ALA B 223 O LEU B 249 SHEET 6 AA7 7 ARG B 160 LEU B 164 1 N MET B 162 O ILE B 222 SHEET 7 AA7 7 GLU B 191 TYR B 195 1 O GLU B 191 N ILE B 161 SHEET 1 AA8 4 SER B 371 LEU B 372 0 SHEET 2 AA8 4 LEU B 381 ASP B 385 -1 O ASP B 385 N SER B 371 SHEET 3 AA8 4 GLY B 423 GLY B 427 -1 O LEU B 424 N VAL B 384 SHEET 4 AA8 4 ASN B 408 ASN B 410 -1 N ASN B 408 O ARG B 425 LINK NZ LYS A 280 C4A PLP A 605 1555 1555 1.45 LINK NZ LYS B 280 C4A PLP B 603 1555 1555 1.45 CISPEP 1 PHE A 320 PRO A 321 0 18.39 CISPEP 2 PHE B 320 PRO B 321 0 16.78 SITE 1 AC1 7 LYS A 200 THR A 201 SER A 374 GLY A 375 SITE 2 AC1 7 HOH A 711 HOH A 755 HOH A 832 SITE 1 AC2 4 ARG A 219 LYS A 245 HIS A 247 HOH A 713 SITE 1 AC3 4 THR A 201 ARG A 230 SER A 374 HOH A 712 SITE 1 AC4 1 ILE A 264 SITE 1 AC5 17 SER A 142 GLY A 143 SER A 144 HIS A 171 SITE 2 AC5 17 THR A 225 SER A 226 ASP A 251 ALA A 253 SITE 3 AC5 17 HIS A 254 THR A 277 HIS A 279 LYS A 280 SITE 4 AC5 17 TYR B 96 GLY B 325 GLY B 326 HOH B 766 SITE 5 AC5 17 HOH B 776 SITE 1 AC6 8 ALA B 223 GLY B 224 THR B 225 ILE B 232 SITE 2 AC6 8 TYR B 234 ASP B 251 MET B 252 PLP B 603 SITE 1 AC7 7 LEU A 166 LYS A 181 ILE A 183 ARG A 425 SITE 2 AC7 7 GLU B 98 TYR B 105 TYR B 106 SITE 1 AC8 23 TYR A 96 GLY A 325 GLY A 326 HOH A 754 SITE 2 AC8 23 HOH A 762 SER B 76 ASN B 78 SER B 142 SITE 3 AC8 23 GLY B 143 SER B 144 HIS B 171 THR B 225 SITE 4 AC8 23 SER B 226 ASP B 251 ALA B 253 HIS B 254 SITE 5 AC8 23 THR B 277 HIS B 279 THR B 281 LEU B 282 SITE 6 AC8 23 ARG B 283 GOL B 601 HOH B 760 CRYST1 160.208 160.208 209.442 90.00 90.00 120.00 P 65 2 2 24 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 0.006242 0.003604 0.000000 0.00000 SCALE2 0.000000 0.007207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004775 0.00000