HEADER TRANSFERASE 09-JUN-23 8T4O TITLE HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASE (SHMT2) IN COMPLEX TITLE 2 WITH PLP, GLYCINE AND AGF347 INHIBITOR WITH NO GLUTAMATE 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MITOCHONDRIAL, ONE-CARBON METABOLISM, POLYGLUTAMATE, INHIBITOR, KEYWDS 2 COMPLEX, SERINE AND GLYCINE METABOLISM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KATINAS,C.E.DANN III REVDAT 1 21-FEB-24 8T4O 0 JRNL AUTH J.M.KATINAS,M.J.NAYEEN,M.SCHNEIDER,K.SHAH,A.N.FIFER, JRNL AUTH 2 L.M.KLAPPER,A.SHARMA,K.THALLURI,M.S.VAN NIEUWENHZE,Z.HOU, JRNL AUTH 3 A.GANGJEE,L.H.MATHERLY,C.E.DANN 3RD JRNL TITL STRUCTURAL CHARACTERIZATION OF 5-SUBSTITUTED PYRROLO[3,2- D JRNL TITL 2 ]PYRIMIDINE ANTIFOLATE INHIBITORS IN COMPLEX WITH HUMAN JRNL TITL 3 SERINE HYDROXYMETHYL TRANSFERASE 2. JRNL REF BIOCHEMISTRY 2024 JRNL REFN ISSN 0006-2960 JRNL PMID 38324671 JRNL DOI 10.1021/ACS.BIOCHEM.3C00613 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 43534 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2190 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.7830 - 5.7711 1.00 4477 226 0.1975 0.2272 REMARK 3 2 5.7711 - 4.5818 1.00 4232 231 0.1822 0.2025 REMARK 3 3 4.5818 - 4.0030 1.00 4197 211 0.1795 0.2220 REMARK 3 4 4.0030 - 3.6371 1.00 4157 220 0.1867 0.2334 REMARK 3 5 3.6371 - 3.3765 1.00 4115 221 0.2165 0.2570 REMARK 3 6 3.3765 - 3.1774 1.00 4120 220 0.2454 0.3225 REMARK 3 7 3.1774 - 3.0183 1.00 4105 222 0.2648 0.3432 REMARK 3 8 3.0183 - 2.8870 1.00 4089 218 0.2661 0.3116 REMARK 3 9 2.8870 - 2.7758 0.99 4062 214 0.2840 0.3306 REMARK 3 10 2.7758 - 2.6801 0.93 3790 207 0.3245 0.3850 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 7264 REMARK 3 ANGLE : 0.616 9839 REMARK 3 CHIRALITY : 0.040 1078 REMARK 3 PLANARITY : 0.003 1295 REMARK 3 DIHEDRAL : 3.995 6006 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -19.1929 65.4117 6.6756 REMARK 3 T TENSOR REMARK 3 T11: 0.2603 T22: 0.5684 REMARK 3 T33: 0.3036 T12: -0.1818 REMARK 3 T13: -0.1137 T23: 0.0509 REMARK 3 L TENSOR REMARK 3 L11: 1.2219 L22: 1.0812 REMARK 3 L33: 2.0500 L12: -0.0350 REMARK 3 L13: 0.8867 L23: -0.8128 REMARK 3 S TENSOR REMARK 3 S11: -0.2315 S12: 0.1172 S13: 0.1089 REMARK 3 S21: 0.2920 S22: -0.1011 S23: -0.2407 REMARK 3 S31: -0.3503 S32: 0.6592 S33: 0.0640 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8T4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000274968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 48.783 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.46800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 2.03100 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 (%): 64.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM PHOSPHATE PH 7.5, 100 MM REMARK 280 NACL, 0.2 MM EDTA, AND 0.5 MM TCEP AND PLP LOADED HIS-SHMT2 REMARK 280 CONCENTRATED TO 0.01 TO 0.02 MM, BATCH MODE, TEMPERATURE 277K 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 138.67267 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 69.33633 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 104.00450 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 34.66817 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 173.34083 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 138.67267 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 69.33633 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 34.66817 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 104.00450 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 173.34083 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 350 BIOMT1 2 0.500000 0.866025 0.000000 -79.26900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 137.29794 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -34.66817 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 12 REMARK 465 GLY A 13 REMARK 465 SER A 14 REMARK 465 SER A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 GLY A 24 REMARK 465 LEU A 25 REMARK 465 VAL A 26 REMARK 465 PRO A 27 REMARK 465 ARG 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 VAL A 299 REMARK 465 ASP A 300 REMARK 465 PRO A 301 REMARK 465 LYS A 302 REMARK 465 ARG A 305 REMARK 465 SER A 417 REMARK 465 ALA A 418 REMARK 465 MET B 12 REMARK 465 GLY B 13 REMARK 465 SER B 14 REMARK 465 SER B 15 REMARK 465 HIS B 16 REMARK 465 HIS B 17 REMARK 465 HIS B 18 REMARK 465 HIS B 19 REMARK 465 HIS B 20 REMARK 465 HIS B 21 REMARK 465 SER B 22 REMARK 465 SER B 23 REMARK 465 GLY B 24 REMARK 465 LEU B 25 REMARK 465 VAL B 26 REMARK 465 PRO B 27 REMARK 465 ARG 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 ALA B 418 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 ILE A 307 CG1 CG2 CD1 REMARK 470 ASP A 415 CG OD1 OD2 REMARK 470 ILE A 419 CG1 CG2 CD1 REMARK 470 LYS A 464 CG CD CE NZ REMARK 470 LYS B 297 CG CD CE NZ REMARK 470 PRO B 301 CG CD REMARK 470 LYS B 302 CG CD CE NZ REMARK 470 THR B 303 OG1 CG2 REMARK 470 ARG B 305 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 368 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 389 CG CD CE NZ REMARK 470 LEU B 391 CG CD1 CD2 REMARK 470 ASP B 392 CG OD1 OD2 REMARK 470 ASN B 410 CG OD1 ND2 REMARK 470 CYS B 412 SG REMARK 470 ASP B 415 CG OD1 OD2 REMARK 470 ARG B 416 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 419 CG1 CG2 CD1 REMARK 470 THR B 420 OG1 CG2 REMARK 470 GLU B 457 CG CD OE1 OE2 REMARK 470 LYS B 459 CG CD CE NZ REMARK 470 LYS B 461 CG CD CE NZ REMARK 470 LYS B 464 CG CD CE NZ REMARK 470 GLN B 466 CG CD OE1 NE2 REMARK 470 LYS B 469 CG CD CE NZ REMARK 470 PHE B 471 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 472 CG CD1 CD2 REMARK 470 LEU B 473 CG CD1 CD2 REMARK 470 THR B 478 OG1 CG2 REMARK 470 LEU B 482 CG CD1 CD2 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 NH2 ARG B 230 O SER B 374 1.71 REMARK 500 NH2 ARG B 230 C SER B 374 2.06 REMARK 500 O GLN B 466 OG SER B 470 2.18 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 LYS A 103 47.04 -107.59 REMARK 500 TYR A 106 -152.95 -108.37 REMARK 500 ALA A 109 41.05 -88.02 REMARK 500 MET A 252 33.34 -93.89 REMARK 500 HIS A 270 -13.26 -140.53 REMARK 500 HIS A 279 -150.06 -87.08 REMARK 500 LYS A 280 -133.47 61.50 REMARK 500 ASN A 379 -136.61 -129.47 REMARK 500 ALA A 407 -168.24 -124.44 REMARK 500 ALA A 463 -81.40 -111.42 REMARK 500 PRO B 131 2.52 -64.02 REMARK 500 SER B 178 -145.18 -80.62 REMARK 500 PRO B 199 5.06 -67.88 REMARK 500 ALA B 223 79.91 -102.20 REMARK 500 LYS B 245 76.48 43.22 REMARK 500 ASP B 251 77.37 -104.68 REMARK 500 MET B 252 28.24 -76.03 REMARK 500 HIS B 279 -143.34 -93.67 REMARK 500 LYS B 280 -123.22 61.04 REMARK 500 LYS B 302 -143.37 57.80 REMARK 500 ARG B 368 -160.19 -129.35 REMARK 500 SER B 374 -17.51 66.53 REMARK 500 ASN B 379 -126.23 -128.23 REMARK 500 SER B 404 37.97 74.14 REMARK 500 ARG B 416 -158.28 -124.28 REMARK 500 THR B 420 76.83 -114.81 REMARK 500 THR B 462 -151.17 -122.64 REMARK 500 ALA B 463 -90.65 -143.24 REMARK 500 SER B 470 -70.94 -67.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 8T4O A 29 504 UNP P34897 GLYM_HUMAN 29 504 DBREF 8T4O B 29 504 UNP P34897 GLYM_HUMAN 29 504 SEQADV 8T4O MET A 12 UNP P34897 INITIATING METHIONINE SEQADV 8T4O GLY A 13 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER A 14 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER A 15 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS A 16 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS A 17 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS A 18 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS A 19 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS A 20 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS A 21 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER A 22 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER A 23 UNP P34897 EXPRESSION TAG SEQADV 8T4O GLY A 24 UNP P34897 EXPRESSION TAG SEQADV 8T4O LEU A 25 UNP P34897 EXPRESSION TAG SEQADV 8T4O VAL A 26 UNP P34897 EXPRESSION TAG SEQADV 8T4O PRO A 27 UNP P34897 EXPRESSION TAG SEQADV 8T4O ARG A 28 UNP P34897 EXPRESSION TAG SEQADV 8T4O MET B 12 UNP P34897 INITIATING METHIONINE SEQADV 8T4O GLY B 13 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER B 14 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER B 15 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS B 16 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS B 17 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS B 18 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS B 19 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS B 20 UNP P34897 EXPRESSION TAG SEQADV 8T4O HIS B 21 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER B 22 UNP P34897 EXPRESSION TAG SEQADV 8T4O SER B 23 UNP P34897 EXPRESSION TAG SEQADV 8T4O GLY B 24 UNP P34897 EXPRESSION TAG SEQADV 8T4O LEU B 25 UNP P34897 EXPRESSION TAG SEQADV 8T4O VAL B 26 UNP P34897 EXPRESSION TAG SEQADV 8T4O PRO B 27 UNP P34897 EXPRESSION TAG SEQADV 8T4O ARG B 28 UNP P34897 EXPRESSION TAG SEQRES 1 A 493 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 493 LEU VAL PRO ARG SER ASN ALA ALA GLN THR GLN THR GLY SEQRES 3 A 493 GLU ALA ASN ARG GLY TRP THR GLY GLN GLU SER LEU SER SEQRES 4 A 493 ASP SER ASP PRO GLU MET TRP GLU LEU LEU GLN ARG GLU SEQRES 5 A 493 LYS ASP ARG GLN CYS ARG GLY LEU GLU LEU ILE ALA SER SEQRES 6 A 493 GLU ASN PHE CYS SER ARG ALA ALA LEU GLU ALA LEU GLY SEQRES 7 A 493 SER CYS LEU ASN ASN LYS TYR SER GLU GLY TYR PRO GLY SEQRES 8 A 493 LYS ARG TYR TYR GLY GLY ALA GLU VAL VAL ASP GLU ILE SEQRES 9 A 493 GLU LEU LEU CYS GLN ARG ARG ALA LEU GLU ALA PHE ASP SEQRES 10 A 493 LEU ASP PRO ALA GLN TRP GLY VAL ASN VAL GLN PRO TYR SEQRES 11 A 493 SER GLY SER PRO ALA ASN LEU ALA VAL TYR THR ALA LEU SEQRES 12 A 493 LEU GLN PRO HIS ASP ARG ILE MET GLY LEU ASP LEU PRO SEQRES 13 A 493 ASP GLY GLY HIS LEU THR HIS GLY TYR MET SER ASP VAL SEQRES 14 A 493 LYS ARG ILE SER ALA THR SER ILE PHE PHE GLU SER MET SEQRES 15 A 493 PRO TYR LYS LEU ASN PRO LYS THR GLY LEU ILE ASP TYR SEQRES 16 A 493 ASN GLN LEU ALA LEU THR ALA ARG LEU PHE ARG PRO ARG SEQRES 17 A 493 LEU ILE ILE ALA GLY THR SER ALA TYR ALA ARG LEU ILE SEQRES 18 A 493 ASP TYR ALA ARG MET ARG GLU VAL CYS ASP GLU VAL LYS SEQRES 19 A 493 ALA HIS LEU LEU ALA ASP MET ALA HIS ILE SER GLY LEU SEQRES 20 A 493 VAL ALA ALA LYS VAL ILE PRO SER PRO PHE LYS HIS ALA SEQRES 21 A 493 ASP ILE VAL THR THR THR THR HIS LYS THR LEU ARG GLY SEQRES 22 A 493 ALA ARG SER GLY LEU ILE PHE TYR ARG LYS GLY VAL LYS SEQRES 23 A 493 ALA VAL ASP PRO LYS THR GLY ARG GLU ILE PRO TYR THR SEQRES 24 A 493 PHE GLU ASP ARG ILE ASN PHE ALA VAL PHE PRO SER LEU SEQRES 25 A 493 GLN GLY GLY PRO HIS ASN HIS ALA ILE ALA ALA VAL ALA SEQRES 26 A 493 VAL ALA LEU LYS GLN ALA CYS THR PRO MET PHE ARG GLU SEQRES 27 A 493 TYR SER LEU GLN VAL LEU LYS ASN ALA ARG ALA MET ALA SEQRES 28 A 493 ASP ALA LEU LEU GLU ARG GLY TYR SER LEU VAL SER GLY SEQRES 29 A 493 GLY THR ASP ASN HIS LEU VAL LEU VAL ASP LEU ARG PRO SEQRES 30 A 493 LYS GLY LEU ASP GLY ALA ARG ALA GLU ARG VAL LEU GLU SEQRES 31 A 493 LEU VAL SER ILE THR ALA ASN LYS ASN THR CYS PRO GLY SEQRES 32 A 493 ASP ARG SER ALA ILE THR PRO GLY GLY LEU ARG LEU GLY SEQRES 33 A 493 ALA PRO ALA LEU THR SER ARG GLN PHE ARG GLU ASP ASP SEQRES 34 A 493 PHE ARG ARG VAL VAL ASP PHE ILE ASP GLU GLY VAL ASN SEQRES 35 A 493 ILE GLY LEU GLU VAL LYS SER LYS THR ALA LYS LEU GLN SEQRES 36 A 493 ASP PHE LYS SER PHE LEU LEU LYS ASP SER GLU THR SER SEQRES 37 A 493 GLN ARG LEU ALA ASN LEU ARG GLN ARG VAL GLU GLN PHE SEQRES 38 A 493 ALA ARG ALA PHE PRO MET PRO GLY PHE ASP GLU HIS SEQRES 1 B 493 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 493 LEU VAL PRO ARG SER ASN ALA ALA GLN THR GLN THR GLY SEQRES 3 B 493 GLU ALA ASN ARG GLY TRP THR GLY GLN GLU SER LEU SER SEQRES 4 B 493 ASP SER ASP PRO GLU MET TRP GLU LEU LEU GLN ARG GLU SEQRES 5 B 493 LYS ASP ARG GLN CYS ARG GLY LEU GLU LEU ILE ALA SER SEQRES 6 B 493 GLU ASN PHE CYS SER ARG ALA ALA LEU GLU ALA LEU GLY SEQRES 7 B 493 SER CYS LEU ASN ASN LYS TYR SER GLU GLY TYR PRO GLY SEQRES 8 B 493 LYS ARG TYR TYR GLY GLY ALA GLU VAL VAL ASP GLU ILE SEQRES 9 B 493 GLU LEU LEU CYS GLN ARG ARG ALA LEU GLU ALA PHE ASP SEQRES 10 B 493 LEU ASP PRO ALA GLN TRP GLY VAL ASN VAL GLN PRO TYR SEQRES 11 B 493 SER GLY SER PRO ALA ASN LEU ALA VAL TYR THR ALA LEU SEQRES 12 B 493 LEU GLN PRO HIS ASP ARG ILE MET GLY LEU ASP LEU PRO SEQRES 13 B 493 ASP GLY GLY HIS LEU THR HIS GLY TYR MET SER ASP VAL SEQRES 14 B 493 LYS ARG ILE SER ALA THR SER ILE PHE PHE GLU SER MET SEQRES 15 B 493 PRO TYR LYS LEU ASN PRO LYS THR GLY LEU ILE ASP TYR SEQRES 16 B 493 ASN GLN LEU ALA LEU THR ALA ARG LEU PHE ARG PRO ARG SEQRES 17 B 493 LEU ILE ILE ALA GLY THR SER ALA TYR ALA ARG LEU ILE SEQRES 18 B 493 ASP TYR ALA ARG MET ARG GLU VAL CYS ASP GLU VAL LYS SEQRES 19 B 493 ALA HIS LEU LEU ALA ASP MET ALA HIS ILE SER GLY LEU SEQRES 20 B 493 VAL ALA ALA LYS VAL ILE PRO SER PRO PHE LYS HIS ALA SEQRES 21 B 493 ASP ILE VAL THR THR THR THR HIS LYS THR LEU ARG GLY SEQRES 22 B 493 ALA ARG SER GLY LEU ILE PHE TYR ARG LYS GLY VAL LYS SEQRES 23 B 493 ALA VAL ASP PRO LYS THR GLY ARG GLU ILE PRO TYR THR SEQRES 24 B 493 PHE GLU ASP ARG ILE ASN PHE ALA VAL PHE PRO SER LEU SEQRES 25 B 493 GLN GLY GLY PRO HIS ASN HIS ALA ILE ALA ALA VAL ALA SEQRES 26 B 493 VAL ALA LEU LYS GLN ALA CYS THR PRO MET PHE ARG GLU SEQRES 27 B 493 TYR SER LEU GLN VAL LEU LYS ASN ALA ARG ALA MET ALA SEQRES 28 B 493 ASP ALA LEU LEU GLU ARG GLY TYR SER LEU VAL SER GLY SEQRES 29 B 493 GLY THR ASP ASN HIS LEU VAL LEU VAL ASP LEU ARG PRO SEQRES 30 B 493 LYS GLY LEU ASP GLY ALA ARG ALA GLU ARG VAL LEU GLU SEQRES 31 B 493 LEU VAL SER ILE THR ALA ASN LYS ASN THR CYS PRO GLY SEQRES 32 B 493 ASP ARG SER ALA ILE THR PRO GLY GLY LEU ARG LEU GLY SEQRES 33 B 493 ALA PRO ALA LEU THR SER ARG GLN PHE ARG GLU ASP ASP SEQRES 34 B 493 PHE ARG ARG VAL VAL ASP PHE ILE ASP GLU GLY VAL ASN SEQRES 35 B 493 ILE GLY LEU GLU VAL LYS SER LYS THR ALA LYS LEU GLN SEQRES 36 B 493 ASP PHE LYS SER PHE LEU LEU LYS ASP SER GLU THR SER SEQRES 37 B 493 GLN ARG LEU ALA ASN LEU ARG GLN ARG VAL GLU GLN PHE SEQRES 38 B 493 ALA ARG ALA PHE PRO MET PRO GLY PHE ASP GLU HIS HET Y5C A 601 25 HET PLG A 602 20 HET PLG B 601 20 HETNAM Y5C 4-[4-(2-AMINO-4-OXO-3,4-DIHYDRO-5H-PYRROLO[3,2- HETNAM 2 Y5C D]PYRIMIDIN-5-YL)BUTYL]-2-FLUOROBENZOIC ACID HETNAM PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- HETNAM 2 PLG PYRIDIN-4-YL-METHANE] HETSYN PLG N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE FORMUL 3 Y5C C17 H17 F N4 O3 FORMUL 4 PLG 2(C10 H15 N2 O7 P) FORMUL 6 HOH *23(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 ASP A 165 GLY A 169 5 5 HELIX 8 AA8 HIS A 171 GLY A 175 5 5 HELIX 9 AA9 SER A 184 ILE A 188 5 5 HELIX 10 AB1 ASP A 205 ARG A 217 1 13 HELIX 11 AB2 ASP A 233 VAL A 244 1 12 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 CYS A 343 1 16 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 ASP A 392 VAL A 403 1 12 HELIX 20 AC2 ALA A 428 SER A 433 1 6 HELIX 21 AC3 ARG A 437 SER A 460 1 24 HELIX 22 AC4 LYS A 464 ASP A 475 1 12 HELIX 23 AC5 ASP A 475 ALA A 495 1 21 HELIX 24 AC6 SER B 48 ASP B 53 1 6 HELIX 25 AC7 ASP B 53 GLY B 70 1 18 HELIX 26 AC8 SER B 81 GLY B 89 1 9 HELIX 27 AC9 SER B 90 LYS B 95 5 6 HELIX 28 AD1 ALA B 109 PHE B 127 1 19 HELIX 29 AD2 SER B 142 LEU B 155 1 14 HELIX 30 AD3 LEU B 166 GLY B 169 5 4 HELIX 31 AD4 HIS B 171 GLY B 175 5 5 HELIX 32 AD5 ALA B 185 PHE B 190 1 6 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 SER B 374 GLY B 376 5 3 HELIX 42 AE6 LEU B 386 GLY B 390 5 5 HELIX 43 AE7 ASP B 392 VAL B 403 1 12 HELIX 44 AE8 ALA B 428 SER B 433 1 6 HELIX 45 AE9 ARG B 437 SER B 460 1 24 HELIX 46 AF1 LYS B 464 ASP B 475 1 12 HELIX 47 AF2 ASP B 475 GLN B 480 1 6 HELIX 48 AF3 GLN B 480 ALA B 495 1 16 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 TYR A 292 N GLY A 135 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 MET A 162 1 N MET A 162 O ILE A 222 SHEET 7 AA3 7 GLU A 191 SER A 192 1 O GLU A 191 N ILE A 161 SHEET 1 AA4 2 VAL A 296 ALA A 298 0 SHEET 2 AA4 2 ILE A 307 PRO A 308 -1 O ILE A 307 N LYS A 297 SHEET 1 AA5 4 SER A 371 LEU A 372 0 SHEET 2 AA5 4 LEU A 381 ASP A 385 -1 O ASP A 385 N SER A 371 SHEET 3 AA5 4 GLY A 423 GLY A 427 -1 O LEU A 424 N VAL A 384 SHEET 4 AA5 4 ASN A 408 ASN A 410 -1 N ASN A 408 O ARG A 425 SHEET 1 AA6 2 LEU B 71 GLU B 72 0 SHEET 2 AA6 2 ILE B 405 THR B 406 1 O THR B 406 N LEU B 71 SHEET 1 AA7 2 GLY B 99 TYR B 100 0 SHEET 2 AA7 2 LYS B 103 ARG B 104 -1 O LYS B 103 N TYR B 100 SHEET 1 AA8 7 TRP B 134 ASN B 137 0 SHEET 2 AA8 7 GLY B 288 ARG B 293 -1 O TYR B 292 N GLY B 135 SHEET 3 AA8 7 ILE B 273 THR B 277 -1 N VAL B 274 O PHE B 291 SHEET 4 AA8 7 HIS B 247 ASP B 251 1 N ALA B 250 O ILE B 273 SHEET 5 AA8 7 LEU B 220 ILE B 222 1 N ILE B 221 O HIS B 247 SHEET 6 AA8 7 ARG B 160 LEU B 164 1 N MET B 162 O ILE B 222 SHEET 7 AA8 7 GLU B 191 TYR B 195 1 O GLU B 191 N ILE B 161 SHEET 1 AA9 2 VAL B 296 ALA B 298 0 SHEET 2 AA9 2 ILE B 307 PRO B 308 -1 O ILE B 307 N ALA B 298 SHEET 1 AB1 4 SER B 371 LEU B 372 0 SHEET 2 AB1 4 LEU B 381 ASP B 385 -1 O ASP B 385 N SER B 371 SHEET 3 AB1 4 LEU B 424 GLY B 427 -1 O LEU B 426 N VAL B 382 SHEET 4 AB1 4 ASN B 408 LYS B 409 -1 N ASN B 408 O ARG B 425 CISPEP 1 PHE A 320 PRO A 321 0 7.40 CISPEP 2 PHE B 320 PRO B 321 0 8.66 CRYST1 158.538 158.538 208.009 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 0.006308 0.003642 0.000000 0.00000 SCALE2 0.000000 0.007283 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004807 0.00000