HEADER TRANSFERASE/INHIBITOR 20-MAR-23 8GKT TITLE HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASE (SHMT2) IN COMPLEX TITLE 2 WITH PLP, GLYCINE AND AGF320 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 8GKT 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. 2.64 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) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 45449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2243 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 48.6450 - 5.6850 1.00 4620 252 0.1967 0.2582 REMARK 3 2 5.6850 - 4.5134 1.00 4381 244 0.1708 0.2117 REMARK 3 3 4.5134 - 3.9432 1.00 4344 225 0.1581 0.1940 REMARK 3 4 3.9432 - 3.5828 1.00 4299 247 0.1737 0.2195 REMARK 3 5 3.5828 - 3.3260 1.00 4295 227 0.1980 0.2697 REMARK 3 6 3.3260 - 3.1300 1.00 4275 220 0.2202 0.2811 REMARK 3 7 3.1300 - 2.9732 1.00 4252 223 0.2411 0.2831 REMARK 3 8 2.9732 - 2.8438 1.00 4271 198 0.2487 0.2716 REMARK 3 9 2.8438 - 2.7344 1.00 4266 201 0.2716 0.3032 REMARK 3 10 2.7344 - 2.6400 0.99 4203 206 0.3055 0.3328 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.860 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 7308 REMARK 3 ANGLE : 0.725 9913 REMARK 3 CHIRALITY : 0.045 1083 REMARK 3 PLANARITY : 0.004 1295 REMARK 3 DIHEDRAL : 5.885 4356 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): -19.4612 65.0292 6.3791 REMARK 3 T TENSOR REMARK 3 T11: 0.2232 T22: 0.6350 REMARK 3 T33: 0.3117 T12: -0.1665 REMARK 3 T13: -0.1095 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 1.0700 L22: 1.0324 REMARK 3 L33: 1.9790 L12: 0.0155 REMARK 3 L13: 0.6929 L23: -0.6604 REMARK 3 S TENSOR REMARK 3 S11: -0.1594 S12: 0.0416 S13: 0.1022 REMARK 3 S21: 0.2598 S22: -0.0911 S23: -0.2491 REMARK 3 S31: -0.2760 S32: 0.7420 S33: 0.0204 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 8GKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000270961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-19 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 : 45564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.640 REMARK 200 RESOLUTION RANGE LOW (A) : 48.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.34500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 2.57600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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 (%): 64.12 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 138.18600 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 69.09300 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 103.63950 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 34.54650 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 172.73250 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 138.18600 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 69.09300 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 34.54650 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 103.63950 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 172.73250 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 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 0.500000 0.866025 0.000000 -79.09800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 137.00175 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -34.54650 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 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 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 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 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 THR A 303 OG1 CG2 REMARK 470 ARG A 437 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 464 CG CD CE NZ REMARK 470 ARG B 230 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 236 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 239 CG CD OE1 OE2 REMARK 470 LYS B 262 CG CD CE NZ REMARK 470 ILE B 264 CG1 CG2 CD1 REMARK 470 LYS B 269 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 GLU B 349 CG CD OE1 OE2 REMARK 470 ARG B 359 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 367 CG CD OE1 OE2 REMARK 470 ARG B 368 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 389 CG CD CE NZ REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 399 CG1 CG2 REMARK 470 ARG B 416 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 459 CG CD CE NZ REMARK 470 LYS B 461 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 473 CG CD1 CD2 REMARK 470 GLU B 477 CG CD OE1 OE2 REMARK 470 GLN B 480 CG CD OE1 NE2 REMARK 470 ARG B 481 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 484 CG OD1 ND2 REMARK 470 ARG B 486 CG CD NE CZ NH1 NH2 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 OG SER B 142 OP1 PLG B 601 2.06 REMARK 500 O GLU B 367 N GLY B 369 2.19 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 57.43 -143.31 REMARK 500 TYR A 106 -169.55 -120.49 REMARK 500 THR A 173 4.30 -68.66 REMARK 500 LYS A 280 -120.91 -100.31 REMARK 500 ASN A 379 -141.97 -133.21 REMARK 500 ALA A 463 -93.32 -114.64 REMARK 500 SER B 97 49.98 -140.20 REMARK 500 TYR B 106 -167.20 -123.44 REMARK 500 THR B 173 4.85 -68.29 REMARK 500 HIS B 279 -146.68 -97.02 REMARK 500 LYS B 280 -128.63 62.57 REMARK 500 GLU B 367 -134.43 -67.70 REMARK 500 ARG B 368 -63.73 34.69 REMARK 500 ASN B 379 -141.27 -132.75 REMARK 500 PRO B 388 43.75 -73.19 REMARK 500 LYS B 389 10.62 -156.01 REMARK 500 ALA B 463 -80.48 -113.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GKT A 29 504 UNP P34897 GLYM_HUMAN 29 504 DBREF 8GKT B 29 504 UNP P34897 GLYM_HUMAN 29 504 SEQADV 8GKT MET A 12 UNP P34897 INITIATING METHIONINE SEQADV 8GKT GLY A 13 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER A 14 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER A 15 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS A 16 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS A 17 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS A 18 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS A 19 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS A 20 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS A 21 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER A 22 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER A 23 UNP P34897 EXPRESSION TAG SEQADV 8GKT GLY A 24 UNP P34897 EXPRESSION TAG SEQADV 8GKT LEU A 25 UNP P34897 EXPRESSION TAG SEQADV 8GKT VAL A 26 UNP P34897 EXPRESSION TAG SEQADV 8GKT PRO A 27 UNP P34897 EXPRESSION TAG SEQADV 8GKT ARG A 28 UNP P34897 EXPRESSION TAG SEQADV 8GKT MET B 12 UNP P34897 INITIATING METHIONINE SEQADV 8GKT GLY B 13 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER B 14 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER B 15 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS B 16 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS B 17 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS B 18 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS B 19 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS B 20 UNP P34897 EXPRESSION TAG SEQADV 8GKT HIS B 21 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER B 22 UNP P34897 EXPRESSION TAG SEQADV 8GKT SER B 23 UNP P34897 EXPRESSION TAG SEQADV 8GKT GLY B 24 UNP P34897 EXPRESSION TAG SEQADV 8GKT LEU B 25 UNP P34897 EXPRESSION TAG SEQADV 8GKT VAL B 26 UNP P34897 EXPRESSION TAG SEQADV 8GKT PRO B 27 UNP P34897 EXPRESSION TAG SEQADV 8GKT 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 PLG A 601 20 HET Y7L A 602 66 HET PLG B 601 20 HET Y7L B 602 66 HETNAM PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- HETNAM 2 PLG PYRIDIN-4-YL-METHANE] HETNAM Y7L N-{5-[5-(2-AMINO-4-OXO-3,4-DIHYDRO-5H-PYRROLO[3,2- HETNAM 2 Y7L D]PYRIMIDIN-5-YL)PENTYL]THIOPHENE-2-CARBONYL}-L- HETNAM 3 Y7L GLUTAMIC ACID HETSYN PLG N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE FORMUL 3 PLG 2(C10 H15 N2 O7 P) FORMUL 4 Y7L 2(C21 H25 N5 O6 S) FORMUL 7 HOH *168(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 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 THR A 310 PHE A 320 1 11 HELIX 15 AB6 HIS A 328 CYS A 343 1 16 HELIX 16 AB7 THR A 344 ARG A 368 1 25 HELIX 17 AB8 ARG A 387 GLY A 390 5 4 HELIX 18 AB9 ASP A 392 LEU A 402 1 11 HELIX 19 AC1 ALA A 428 ARG A 434 1 7 HELIX 20 AC2 ARG A 437 THR A 462 1 26 HELIX 21 AC3 LYS A 464 ASP A 475 1 12 HELIX 22 AC4 ASP A 475 ALA A 495 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 ILE B 188 5 5 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 THR B 310 PHE B 320 1 11 HELIX 37 AE1 HIS B 328 CYS B 343 1 16 HELIX 38 AE2 THR B 344 GLU B 367 1 24 HELIX 39 AE3 ARG B 387 GLY B 390 5 4 HELIX 40 AE4 ASP B 392 VAL B 403 1 12 HELIX 41 AE5 ALA B 428 ARG B 434 1 7 HELIX 42 AE6 ARG B 437 SER B 460 1 24 HELIX 43 AE7 LYS B 464 ASP B 475 1 12 HELIX 44 AE8 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 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 THR A 275 SHEET 5 AA3 7 LEU A 220 GLY A 224 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 426 N VAL A 382 SHEET 4 AA4 4 ASN A 408 ASN A 410 -1 N ASN A 410 O GLY A 423 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 THR B 275 SHEET 5 AA7 7 LEU B 220 ALA B 223 1 N ILE B 221 O HIS B 247 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 TYR B 195 N GLY B 163 SHEET 1 AA8 2 VAL B 296 LYS B 297 0 SHEET 2 AA8 2 ILE B 307 PRO B 308 -1 O ILE B 307 N LYS B 297 SHEET 1 AA9 4 SER B 371 LEU B 372 0 SHEET 2 AA9 4 LEU B 381 ASP B 385 -1 O ASP B 385 N SER B 371 SHEET 3 AA9 4 GLY B 423 GLY B 427 -1 O LEU B 426 N VAL B 382 SHEET 4 AA9 4 ASN B 408 ASN B 410 -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 6.74 CRYST1 158.196 158.196 207.279 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 0.004824 0.00000