HEADER TRANSFERASE/INHIBITOR 20-MAR-23 8GKW TITLE HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASE (SHMT2) IN COMPLEX TITLE 2 WITH PLP, GLYCINE AND AGF359 INHIBITOR 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 SHMT2, TETRAMER, GLYCINE SYNTHESIS, INHIBITOR, TRANSFERASE, KEYWDS 2 TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KATINAS,C.E.DANN III REVDAT 1 20-MAR-24 8GKW 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. 2.38 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 61090 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 3036 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 48.4260 - 6.6634 1.00 2916 160 0.1847 0.1897 REMARK 3 2 6.6634 - 5.2910 1.00 2760 144 0.1976 0.2334 REMARK 3 3 5.2910 - 4.6228 1.00 2745 133 0.1636 0.2015 REMARK 3 4 4.6228 - 4.2004 1.00 2694 135 0.1541 0.1792 REMARK 3 5 4.2004 - 3.8995 1.00 2659 159 0.1564 0.2076 REMARK 3 6 3.8995 - 3.6696 1.00 2645 154 0.1651 0.1848 REMARK 3 7 3.6696 - 3.4859 1.00 2680 134 0.1682 0.2100 REMARK 3 8 3.4859 - 3.3342 1.00 2661 126 0.1911 0.2445 REMARK 3 9 3.3342 - 3.2059 1.00 2662 129 0.2008 0.2127 REMARK 3 10 3.2059 - 3.0953 1.00 2634 141 0.1890 0.2257 REMARK 3 11 3.0953 - 2.9985 1.00 2668 130 0.2027 0.2380 REMARK 3 12 2.9985 - 2.9128 1.00 2622 138 0.1946 0.2378 REMARK 3 13 2.9128 - 2.8361 1.00 2635 148 0.2021 0.2622 REMARK 3 14 2.8361 - 2.7669 1.00 2613 156 0.2085 0.2409 REMARK 3 15 2.7669 - 2.7041 1.00 2627 133 0.2204 0.2442 REMARK 3 16 2.7041 - 2.6465 1.00 2616 142 0.2287 0.2889 REMARK 3 17 2.6465 - 2.5936 1.00 2601 137 0.2248 0.2890 REMARK 3 18 2.5936 - 2.5446 0.99 2603 134 0.2354 0.2626 REMARK 3 19 2.5446 - 2.4992 0.97 2541 146 0.2414 0.3165 REMARK 3 20 2.4992 - 2.4568 0.96 2529 113 0.2460 0.3210 REMARK 3 21 2.4568 - 2.4172 0.95 2498 117 0.2535 0.2767 REMARK 3 22 2.4172 - 2.3800 0.93 2445 127 0.2526 0.2553 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.750 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 : 0.002 7296 REMARK 3 ANGLE : 0.534 9875 REMARK 3 CHIRALITY : 0.038 1082 REMARK 3 PLANARITY : 0.003 1295 REMARK 3 DIHEDRAL : 2.748 6085 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): -19.0661 65.0731 6.7109 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.4143 REMARK 3 T33: 0.2388 T12: -0.0727 REMARK 3 T13: -0.0520 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.9468 L22: 0.8127 REMARK 3 L33: 1.3583 L12: 0.1357 REMARK 3 L13: 0.2432 L23: -0.2675 REMARK 3 S TENSOR REMARK 3 S11: -0.0276 S12: -0.0709 S13: 0.0249 REMARK 3 S21: 0.1361 S22: -0.0175 S23: -0.1625 REMARK 3 S31: -0.1023 S32: 0.4003 S33: -0.0038 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 8GKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000270963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-20 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 : 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) : 1.000 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 : 82023 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 48.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.70100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 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 (%): 63.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 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 138.04800 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 69.02400 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 103.53600 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 34.51200 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 172.56000 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 138.04800 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 69.02400 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 34.51200 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 103.53600 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 172.56000 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: 24120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 56910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 -79.09750 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 137.00089 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -34.51200 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 894 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 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 297A REMARK 465 VAL A 297B REMARK 465 ASP A 297C REMARK 465 PRO A 297D REMARK 465 LYS A 297E REMARK 465 THR A 297F REMARK 465 GLY A 297G REMARK 465 ARG A 297H REMARK 465 GLU A 297I REMARK 465 ALA A 408A 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 297A REMARK 465 VAL B 297B REMARK 465 ASP B 297C REMARK 465 PRO B 297D REMARK 465 LYS B 297E REMARK 465 THR B 297F REMARK 465 GLY B 297G REMARK 465 GLY B 406A 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 ARG B 230 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 298 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 408 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 411 CG1 CG2 CD1 REMARK 470 LYS B 461 CG CD CE NZ REMARK 470 PHE B 463 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 465 CG CD1 CD2 REMARK 470 LYS B 466 CG CD CE NZ 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 70.83 -117.71 REMARK 500 THR A 173 3.11 -68.08 REMARK 500 HIS A 279 -142.51 -92.51 REMARK 500 LYS A 280 -130.67 55.48 REMARK 500 ASN A 370 -138.12 -133.06 REMARK 500 ARG A 407 60.38 -117.44 REMARK 500 ALA A 453 -84.28 -106.31 REMARK 500 THR B 173 6.70 -68.68 REMARK 500 SER B 178 -154.40 -79.48 REMARK 500 HIS B 279 -146.82 -93.62 REMARK 500 LYS B 280 -125.89 55.27 REMARK 500 ASN B 372 -133.37 -130.09 REMARK 500 PRO B 381 28.58 -71.65 REMARK 500 ARG B 408 -57.14 -129.72 REMARK 500 ALA B 410 -31.54 -134.25 REMARK 500 ALA B 455 -92.49 -93.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 903 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 904 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 905 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 906 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A 907 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH B 955 DISTANCE = 5.89 ANGSTROMS DBREF 8GKW A 29 494 UNP P34897 GLYM_HUMAN 29 504 DBREF 8GKW B 29 496 UNP P34897 GLYM_HUMAN 29 504 SEQADV 8GKW MET A 12 UNP P34897 INITIATING METHIONINE SEQADV 8GKW GLY A 13 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER A 14 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER A 15 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS A 16 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS A 17 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS A 18 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS A 19 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS A 20 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS A 21 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER A 22 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER A 23 UNP P34897 EXPRESSION TAG SEQADV 8GKW GLY A 24 UNP P34897 EXPRESSION TAG SEQADV 8GKW LEU A 25 UNP P34897 EXPRESSION TAG SEQADV 8GKW VAL A 26 UNP P34897 EXPRESSION TAG SEQADV 8GKW PRO A 27 UNP P34897 EXPRESSION TAG SEQADV 8GKW ARG A 28 UNP P34897 EXPRESSION TAG SEQADV 8GKW MET B 12 UNP P34897 INITIATING METHIONINE SEQADV 8GKW GLY B 13 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER B 14 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER B 15 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS B 16 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS B 17 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS B 18 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS B 19 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS B 20 UNP P34897 EXPRESSION TAG SEQADV 8GKW HIS B 21 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER B 22 UNP P34897 EXPRESSION TAG SEQADV 8GKW SER B 23 UNP P34897 EXPRESSION TAG SEQADV 8GKW GLY B 24 UNP P34897 EXPRESSION TAG SEQADV 8GKW LEU B 25 UNP P34897 EXPRESSION TAG SEQADV 8GKW VAL B 26 UNP P34897 EXPRESSION TAG SEQADV 8GKW PRO B 27 UNP P34897 EXPRESSION TAG SEQADV 8GKW 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 GLY A 601 5 HET PLP A 602 15 HET ZVR B 701 33 HET GLY B 702 5 HET PLP B 703 15 HETNAM GLY GLYCINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM ZVR N-{4-[3-(2-AMINO-4-OXO-3,4-DIHYDRO-5H-PYRROLO[3,2- HETNAM 2 ZVR D]PYRIMIDIN-5-YL)PROPYL]-2-FLUOROBENZOYL}-L-GLUTAMIC HETNAM 3 ZVR ACID HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 GLY 2(C2 H5 N O2) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 5 ZVR C21 H22 F N5 O6 FORMUL 8 HOH *362(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 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 302 PHE A 311 1 10 HELIX 16 AB7 HIS A 319 CYS A 334 1 16 HELIX 17 AB8 THR A 335 ARG A 359 1 25 HELIX 18 AB9 ASP A 383 VAL A 394 1 12 HELIX 19 AC1 ALA A 418 ARG A 424 1 7 HELIX 20 AC2 ARG A 427 LYS A 451 1 25 HELIX 21 AC3 LYS A 454 ASP A 465 1 12 HELIX 22 AC4 ASP A 465 ALA A 485 1 21 HELIX 23 AC5 SER B 48 ASP B 53 1 6 HELIX 24 AC6 ASP B 53 GLY B 70 1 18 HELIX 25 AC7 SER B 81 GLY B 89 1 9 HELIX 26 AC8 SER B 90 LYS B 95 5 6 HELIX 27 AC9 ALA B 109 PHE B 127 1 19 HELIX 28 AD1 SER B 142 LEU B 155 1 14 HELIX 29 AD2 HIS B 171 GLY B 175 5 5 HELIX 30 AD3 SER B 184 PHE B 190 1 7 HELIX 31 AD4 ASP B 205 ARG B 217 1 13 HELIX 32 AD5 ASP B 233 LYS B 245 1 13 HELIX 33 AD6 ILE B 255 ALA B 261 1 7 HELIX 34 AD7 SER B 266 HIS B 270 5 5 HELIX 35 AD8 HIS B 279 ARG B 283 5 5 HELIX 36 AD9 PHE B 304 PHE B 313 1 10 HELIX 37 AE1 HIS B 321 ALA B 335 1 15 HELIX 38 AE2 THR B 337 GLU B 360 1 24 HELIX 39 AE3 LEU B 379 GLY B 383 5 5 HELIX 40 AE4 ASP B 385 LEU B 395 1 11 HELIX 41 AE5 ALA B 420 SER B 425 1 6 HELIX 42 AE6 ARG B 429 THR B 454 1 26 HELIX 43 AE7 LYS B 456 ASP B 467 1 12 HELIX 44 AE8 ASP B 467 ALA B 487 1 21 SHEET 1 AA1 2 LEU A 71 GLU A 72 0 SHEET 2 AA1 2 ILE A 396 THR A 397 1 O THR A 397 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 4 SER A 362 LEU A 363 0 SHEET 2 AA4 4 LEU A 372 ASP A 376 -1 O ASP A 376 N SER A 362 SHEET 3 AA4 4 GLY A 413 GLY A 417 -1 O LEU A 414 N VAL A 375 SHEET 4 AA4 4 ASN A 399 ASN A 401 -1 N ASN A 399 O ARG A 415 SHEET 1 AA5 2 LEU B 71 GLU B 72 0 SHEET 2 AA5 2 ILE B 398 THR B 399 1 O THR B 399 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 THR B 275 SHEET 5 AA7 7 LEU B 220 GLY B 224 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 364 LEU B 365 0 SHEET 2 AA8 4 LEU B 374 ASP B 378 -1 O ASP B 378 N SER B 364 SHEET 3 AA8 4 GLY B 415 GLY B 419 -1 O LEU B 418 N VAL B 375 SHEET 4 AA8 4 ASN B 401 ASN B 403 -1 N ASN B 403 O GLY B 415 LINK NZ LYS A 280 C4A PLP A 602 1555 1555 1.28 LINK NZ ALYS B 280 C4A PLP B 703 1555 1555 1.27 CISPEP 1 PHE A 311 PRO A 312 0 7.60 CISPEP 2 PHE B 313 PRO B 314 0 8.69 CRYST1 158.195 158.195 207.072 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 0.006321 0.003650 0.000000 0.00000 SCALE2 0.000000 0.007299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004829 0.00000