HEADER TRANSFERASE 26-JUL-23 8TLC TITLE HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASE (SHMT2) IN COMPLEX TITLE 2 WITH PLP, GLYCINE AND TRI-GLUTAMATE AGF347 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 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 SHMT2, TETRAMER, GLYCINE SYNTHESIS, INHIBITOR, POLYGLUTAMATE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KATINAS,C.E.DANN III REVDAT 1 21-FEB-24 8TLC 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. 2.72 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 41812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.309 REMARK 3 R VALUE (WORKING SET) : 0.306 REMARK 3 FREE R VALUE : 0.359 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2050 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 48.7120 - 5.8570 1.00 4280 215 0.2411 0.3051 REMARK 3 2 5.8570 - 4.6501 1.00 4045 226 0.2712 0.3063 REMARK 3 3 4.6501 - 4.0626 1.00 4026 186 0.2740 0.3319 REMARK 3 4 4.0626 - 3.6913 0.99 3934 216 0.3192 0.3647 REMARK 3 5 3.6913 - 3.4268 0.99 3931 200 0.3645 0.4201 REMARK 3 6 3.4268 - 3.2248 1.00 3938 191 0.3542 0.4176 REMARK 3 7 3.2248 - 3.0633 1.00 3899 230 0.3515 0.3920 REMARK 3 8 3.0633 - 2.9300 1.00 3924 200 0.3395 0.4186 REMARK 3 9 2.9300 - 2.8172 1.00 3921 198 0.3553 0.3948 REMARK 3 10 2.8172 - 2.7200 0.99 3864 188 0.3617 0.3993 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) : 0.530 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.910 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 : 0.004 7132 REMARK 3 ANGLE : 0.787 9669 REMARK 3 CHIRALITY : 0.044 1066 REMARK 3 PLANARITY : 0.005 1272 REMARK 3 DIHEDRAL : 7.045 4272 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): -19.2733 65.1651 6.6913 REMARK 3 T TENSOR REMARK 3 T11: 0.3495 T22: 0.6912 REMARK 3 T33: -0.1600 T12: -0.1508 REMARK 3 T13: -0.3233 T23: 0.2463 REMARK 3 L TENSOR REMARK 3 L11: 0.8288 L22: 1.1178 REMARK 3 L33: 1.4954 L12: -0.3087 REMARK 3 L13: 0.7724 L23: -0.6150 REMARK 3 S TENSOR REMARK 3 S11: -0.3815 S12: -0.2533 S13: 0.4899 REMARK 3 S21: 0.5157 S22: -0.1296 S23: -0.8565 REMARK 3 S31: -0.3908 S32: 0.3442 S33: -0.1080 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 8TLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000274970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-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 : 41987 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 48.712 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.34100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.07300 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 (%): 64.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 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 138.10333 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 69.05167 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 103.57750 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 34.52583 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 172.62917 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 138.10333 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 69.05167 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 34.52583 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 103.57750 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 172.62917 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: 22080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 60610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 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 -79.35900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 137.45382 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -34.52583 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 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 ARG A 416 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 ALA B 132 REMARK 465 ASP B 272 REMARK 465 ALA B 298 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 ALA B 396 REMARK 465 SER B 417 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 LYS A 200 CG CD CE NZ REMARK 470 LYS A 269 CG CD CE NZ REMARK 470 THR A 303 OG1 CG2 REMARK 470 ILE A 307 CG1 CG2 CD1 REMARK 470 GLU A 367 CG CD OE1 OE2 REMARK 470 LYS A 459 CG CD CE NZ REMARK 470 LYS A 464 CG CD CE NZ REMARK 470 ARG B 69 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 71 CG CD1 CD2 REMARK 470 MET B 193 CG SD CE REMARK 470 ILE B 204 CG1 CG2 CD1 REMARK 470 LEU B 209 CG CD1 CD2 REMARK 470 ARG B 214 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 221 CG1 CG2 CD1 REMARK 470 SER B 226 OG REMARK 470 LYS B 269 CG CD CE NZ REMARK 470 ILE B 273 CG1 CG2 CD1 REMARK 470 ARG B 283 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 297 CG CD CE NZ REMARK 470 ARG B 305 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 306 CG CD OE1 OE2 REMARK 470 ILE B 307 CG1 CG2 CD1 REMARK 470 LYS B 340 CG CD CE NZ REMARK 470 GLU B 349 CG CD OE1 OE2 REMARK 470 GLN B 353 CG CD OE1 NE2 REMARK 470 ARG B 359 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 368 CG CD NE CZ NH1 NH2 REMARK 470 SER B 371 OG REMARK 470 HIS B 380 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 386 CG CD1 CD2 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 VAL B 399 CG1 CG2 REMARK 470 THR B 411 OG1 CG2 REMARK 470 PRO B 413 CG CD REMARK 470 ARG B 416 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 437 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 439 CG OD1 OD2 REMARK 470 LYS B 461 CG CD CE NZ REMARK 470 ASP B 467 CG OD1 OD2 REMARK 470 LYS B 469 CG CD CE NZ REMARK 470 LEU B 472 CG CD1 CD2 REMARK 470 LYS B 474 CG CD CE NZ REMARK 470 ARG B 481 CG CD NE CZ NH1 NH2 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 ASN A 94 30.33 -90.74 REMARK 500 GLU A 98 98.07 -61.03 REMARK 500 PRO A 101 107.58 -55.97 REMARK 500 TYR A 106 -128.35 -104.65 REMARK 500 ALA A 109 37.25 -86.58 REMARK 500 ASP A 128 71.10 47.35 REMARK 500 VAL A 180 -19.19 -140.44 REMARK 500 THR A 201 -33.44 -155.47 REMARK 500 ASP A 205 92.05 -68.26 REMARK 500 ALA A 223 59.17 -109.81 REMARK 500 ALA A 227 79.87 -151.91 REMARK 500 LYS A 245 77.01 51.22 REMARK 500 MET A 252 24.85 -78.77 REMARK 500 ILE A 255 16.89 -145.50 REMARK 500 HIS A 279 -148.33 -94.98 REMARK 500 LLP A 280 -132.55 57.81 REMARK 500 SER A 374 -18.78 77.17 REMARK 500 ASN A 379 -139.43 -129.39 REMARK 500 SER A 404 44.61 75.77 REMARK 500 PRO A 413 107.66 -51.09 REMARK 500 PRO A 421 -178.39 -64.27 REMARK 500 ALA A 463 -64.07 -139.36 REMARK 500 SER A 476 6.40 -65.94 REMARK 500 ASN B 94 30.47 -91.25 REMARK 500 GLU B 98 98.42 -62.85 REMARK 500 PRO B 101 106.33 -56.34 REMARK 500 TYR B 106 -130.26 -106.70 REMARK 500 ALA B 109 39.71 -86.07 REMARK 500 ASP B 128 168.48 -48.20 REMARK 500 LEU B 129 157.43 121.84 REMARK 500 VAL B 180 -19.92 -140.76 REMARK 500 THR B 201 -31.42 -156.27 REMARK 500 ASP B 205 91.91 -69.43 REMARK 500 ARG B 217 58.87 39.14 REMARK 500 ALA B 223 61.57 -113.69 REMARK 500 ALA B 227 79.30 -152.39 REMARK 500 ARG B 230 -168.22 -117.98 REMARK 500 LYS B 245 70.65 49.42 REMARK 500 MET B 252 24.18 -75.65 REMARK 500 ILE B 255 18.59 -144.16 REMARK 500 LYS B 262 15.97 54.75 REMARK 500 HIS B 279 -135.23 -98.33 REMARK 500 LLP B 280 -76.84 57.48 REMARK 500 GLU B 312 -74.87 -126.75 REMARK 500 SER B 374 -21.85 80.14 REMARK 500 ASN B 379 -142.32 -129.80 REMARK 500 SER B 404 43.04 76.04 REMARK 500 ASP B 415 -157.47 -126.16 REMARK 500 PRO B 421 -174.50 -67.25 REMARK 500 THR B 462 -169.38 -129.07 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 8TLC A 29 504 UNP P34897 GLYM_HUMAN 29 504 DBREF 8TLC B 29 504 UNP P34897 GLYM_HUMAN 29 504 SEQADV 8TLC MET A 12 UNP P34897 INITIATING METHIONINE SEQADV 8TLC GLY A 13 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER A 14 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER A 15 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS A 16 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS A 17 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS A 18 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS A 19 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS A 20 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS A 21 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER A 22 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER A 23 UNP P34897 EXPRESSION TAG SEQADV 8TLC GLY A 24 UNP P34897 EXPRESSION TAG SEQADV 8TLC LEU A 25 UNP P34897 EXPRESSION TAG SEQADV 8TLC VAL A 26 UNP P34897 EXPRESSION TAG SEQADV 8TLC PRO A 27 UNP P34897 EXPRESSION TAG SEQADV 8TLC ARG A 28 UNP P34897 EXPRESSION TAG SEQADV 8TLC MET B 12 UNP P34897 INITIATING METHIONINE SEQADV 8TLC GLY B 13 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER B 14 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER B 15 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS B 16 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS B 17 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS B 18 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS B 19 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS B 20 UNP P34897 EXPRESSION TAG SEQADV 8TLC HIS B 21 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER B 22 UNP P34897 EXPRESSION TAG SEQADV 8TLC SER B 23 UNP P34897 EXPRESSION TAG SEQADV 8TLC GLY B 24 UNP P34897 EXPRESSION TAG SEQADV 8TLC LEU B 25 UNP P34897 EXPRESSION TAG SEQADV 8TLC VAL B 26 UNP P34897 EXPRESSION TAG SEQADV 8TLC PRO B 27 UNP P34897 EXPRESSION TAG SEQADV 8TLC 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 LLP 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 LLP 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 MODRES 8TLC LLP A 280 LYS MODIFIED RESIDUE MODRES 8TLC LLP B 280 LYS MODIFIED RESIDUE HET LLP A 280 24 HET LLP B 280 24 HET I6I A 601 52 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM I6I N-{4-[4-(2-AMINO-4-OXO-1,4-DIHYDRO-5H-PYRROLO[3,2- HETNAM 2 I6I D]PYRIMIDIN-5-YL)BUTYL]-2-FLUOROBENZOYL}-D-GAMMA- HETNAM 3 I6I GLUTAMYL-L-GAMMA-GLUTAMYL-D-GLUTAMIC ACID HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 I6I C32 H38 F N7 O12 FORMUL 4 HOH *10(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 SER A 184 PHE A 189 1 6 HELIX 9 AA9 TYR A 206 LEU A 215 1 10 HELIX 10 AB1 ASP A 233 VAL A 244 1 12 HELIX 11 AB2 ILE A 255 ALA A 261 1 7 HELIX 12 AB3 HIS A 279 ARG A 283 5 5 HELIX 13 AB4 THR A 310 PHE A 320 1 11 HELIX 14 AB5 HIS A 328 ALA A 342 1 15 HELIX 15 AB6 THR A 344 ARG A 368 1 25 HELIX 16 AB7 LEU A 386 GLY A 390 5 5 HELIX 17 AB8 ASP A 392 SER A 404 1 13 HELIX 18 AB9 ALA A 428 SER A 433 1 6 HELIX 19 AC1 ARG A 437 THR A 462 1 26 HELIX 20 AC2 ASP A 467 ASP A 475 1 9 HELIX 21 AC3 GLU A 477 ARG A 494 1 18 HELIX 22 AC4 SER B 48 ASP B 53 1 6 HELIX 23 AC5 ASP B 53 GLY B 70 1 18 HELIX 24 AC6 SER B 81 GLY B 89 1 9 HELIX 25 AC7 SER B 90 LYS B 95 5 6 HELIX 26 AC8 ALA B 109 PHE B 127 1 19 HELIX 27 AC9 SER B 142 LEU B 155 1 14 HELIX 28 AD1 LEU B 166 GLY B 169 5 4 HELIX 29 AD2 HIS B 171 GLY B 175 5 5 HELIX 30 AD3 SER B 184 PHE B 189 1 6 HELIX 31 AD4 TYR B 206 LEU B 215 1 10 HELIX 32 AD5 ASP B 233 VAL B 244 1 12 HELIX 33 AD6 MET B 252 HIS B 254 5 3 HELIX 34 AD7 ILE B 255 ALA B 261 1 7 HELIX 35 AD8 GLU B 312 PHE B 320 1 9 HELIX 36 AD9 HIS B 328 ALA B 342 1 15 HELIX 37 AE1 THR B 344 ARG B 368 1 25 HELIX 38 AE2 ARG B 387 GLY B 390 5 4 HELIX 39 AE3 ALA B 394 ARG B 395 5 2 HELIX 40 AE4 GLU B 397 GLU B 397 5 1 HELIX 41 AE5 ARG B 398 LEU B 402 1 5 HELIX 42 AE6 ALA B 428 SER B 433 1 6 HELIX 43 AE7 ARG B 442 THR B 462 1 21 HELIX 44 AE8 ASP B 467 ASP B 475 1 9 HELIX 45 AE9 GLU B 477 ARG B 494 1 18 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 7 TRP A 134 ASN A 137 0 SHEET 2 AA2 7 GLY A 288 ARG A 293 -1 O TYR A 292 N GLY A 135 SHEET 3 AA2 7 ILE A 273 THR A 277 -1 N VAL A 274 O PHE A 291 SHEET 4 AA2 7 HIS A 247 ASP A 251 1 N ALA A 250 O THR A 275 SHEET 5 AA2 7 LEU A 220 GLY A 224 1 N ALA A 223 O LEU A 249 SHEET 6 AA2 7 ARG A 160 LEU A 164 1 N MET A 162 O ILE A 222 SHEET 7 AA2 7 GLU A 191 TYR A 195 1 O GLU A 191 N ILE A 161 SHEET 1 AA3 2 SER A 371 LEU A 372 0 SHEET 2 AA3 2 VAL A 384 ASP A 385 -1 O ASP A 385 N SER A 371 SHEET 1 AA4 2 LEU A 381 VAL A 382 0 SHEET 2 AA4 2 LEU A 426 GLY A 427 -1 O LEU A 426 N VAL A 382 SHEET 1 AA5 2 LYS A 409 ASN A 410 0 SHEET 2 AA5 2 GLY A 423 LEU A 424 -1 O GLY A 423 N ASN A 410 SHEET 1 AA6 3 TRP B 134 ASN B 137 0 SHEET 2 AA6 3 GLY B 288 ARG B 293 -1 O TYR B 292 N GLY B 135 SHEET 3 AA6 3 VAL B 274 THR B 277 -1 N THR B 276 O LEU B 289 SHEET 1 AA7 4 SER B 192 TYR B 195 0 SHEET 2 AA7 4 ILE B 161 LEU B 164 1 N GLY B 163 O TYR B 195 SHEET 3 AA7 4 LEU B 220 GLY B 224 1 O ILE B 222 N MET B 162 SHEET 4 AA7 4 HIS B 247 ASP B 251 1 O LEU B 249 N ALA B 223 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 426 N VAL B 382 SHEET 4 AA8 4 LYS B 409 ASN B 410 -1 N ASN B 410 O GLY B 423 LINK C HIS A 279 N LLP A 280 1555 1555 1.33 LINK C LLP A 280 N THR A 281 1555 1555 1.33 LINK C HIS B 279 N LLP B 280 1555 1555 1.33 LINK C LLP B 280 N THR B 281 1555 1555 1.33 CISPEP 1 PHE A 320 PRO A 321 0 5.70 CISPEP 2 PHE B 320 PRO B 321 0 5.64 CRYST1 158.718 158.718 207.155 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 0.006300 0.003638 0.000000 0.00000 SCALE2 0.000000 0.007275 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004827 0.00000