HEADER LYASE 18-NOV-15 5EUE TITLE S1P LYASE BACTERIAL SURROGATE BOUND TO N-(2-((4-METHOXY-2,5- TITLE 2 DIMETHYLBENZYL)AMINO)-1-PHENYLETHYL)-5-METHYLISOXAZOLE-3-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SPHINGOSINE-1-PHOSPHATE LYASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYMBIOBACTERIUM THERMOPHILUM (STRAIN T / IAM SOURCE 3 14863); SOURCE 4 ORGANISM_TAXID: 292459; SOURCE 5 STRAIN: T / IAM 14863; SOURCE 6 GENE: STH1274; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS S1P LYASE BACTERIAL SURROGATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.ARGIRIADI,D.BANACH,E.RADZIEJEWSKA,S.MARCHIE,J.DIMAURO,J.DINGES, AUTHOR 2 E.DOMINGUEZ,C.HUTCHINS,R.A.JUDGE,K.QUEENEY,G.WALLACE,C.M.HARRIS REVDAT 6 15-NOV-23 5EUE 1 REMARK REVDAT 5 27-SEP-23 5EUE 1 REMARK REVDAT 4 20-JUL-16 5EUE 1 REMARK REVDAT 3 27-APR-16 5EUE 1 JRNL REVDAT 2 06-APR-16 5EUE 1 JRNL REVDAT 1 16-MAR-16 5EUE 0 JRNL AUTH M.A.ARGIRIADI,D.BANACH,E.RADZIEJEWSKA,S.MARCHIE,J.DIMAURO, JRNL AUTH 2 J.DINGES,E.DOMINGUEZ,C.HUTCHINS,R.A.JUDGE,K.QUEENEY, JRNL AUTH 3 G.WALLACE,C.M.HARRIS JRNL TITL CREATION OF A S1P LYASE BACTERIAL SURROGATE FOR JRNL TITL 2 STRUCTURE-BASED DRUG DESIGN. JRNL REF BIOORG.MED.CHEM.LETT. V. 26 2293 2016 JRNL REFN ESSN 1464-3405 JRNL PMID 27013389 JRNL DOI 10.1016/J.BMCL.2016.02.084 REMARK 2 REMARK 2 RESOLUTION. 2.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1168 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.59 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2922 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1920 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2767 REMARK 3 BIN R VALUE (WORKING SET) : 0.1877 REMARK 3 BIN FREE R VALUE : 0.2702 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.70320 REMARK 3 B22 (A**2) : -2.57650 REMARK 3 B33 (A**2) : 0.87330 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.288 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.387 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 7096 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9699 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2238 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 122 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1091 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 7096 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 901 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 8498 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.14 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.86 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5EUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22823 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.830 REMARK 200 RESOLUTION RANGE LOW (A) : 129.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3MAD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M KCSN, 0.1M TRIS, PH 8.3, 18% REMARK 280 PEG 5000 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 42.50700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.14350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 64.80300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.14350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.50700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 64.80300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 0 REMARK 465 PRO A 1 REMARK 465 LEU A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 PHE A 5 REMARK 465 SER A 6 REMARK 465 PRO A 7 REMARK 465 PRO A 8 REMARK 465 LEU A 9 REMARK 465 PRO A 10 REMARK 465 CYS A 11 REMARK 465 ASP A 12 REMARK 465 PRO A 13 REMARK 465 ALA A 14 REMARK 465 ARG A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 PRO A 18 REMARK 465 THR A 19 REMARK 465 PRO A 20 REMARK 465 GLU A 21 REMARK 465 PHE A 22 REMARK 465 PRO A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 LEU A 26 REMARK 465 GLN A 27 REMARK 465 ASP A 28 REMARK 465 TYR A 29 REMARK 465 CYS A 30 REMARK 465 GLU A 31 REMARK 465 ILE A 32 REMARK 465 ARG A 33 REMARK 465 GLY A 34 REMARK 465 ILE A 35 REMARK 465 GLN A 36 REMARK 465 SER A 37 REMARK 465 GLN A 38 REMARK 465 PRO A 39 REMARK 465 PRO A 40 REMARK 465 ALA A 41 REMARK 465 ARG A 42 REMARK 465 ARG A 43 REMARK 465 ASP A 44 REMARK 465 PRO A 45 REMARK 465 THR A 46 REMARK 465 MET A 47 REMARK 465 ASP A 48 REMARK 465 TRP A 49 REMARK 465 LEU A 50 REMARK 465 ALA A 51 REMARK 465 SER A 52 REMARK 465 LEU A 53 REMARK 465 ARG A 54 REMARK 465 SER A 55 REMARK 465 GLN A 56 REMARK 465 HIS A 508 REMARK 465 HIS A 509 REMARK 465 HIS A 510 REMARK 465 HIS A 511 REMARK 465 HIS A 512 REMARK 465 HIS A 513 REMARK 465 MET B 0 REMARK 465 PRO B 1 REMARK 465 LEU B 2 REMARK 465 SER B 3 REMARK 465 ALA B 4 REMARK 465 PHE B 5 REMARK 465 SER B 6 REMARK 465 PRO B 7 REMARK 465 PRO B 8 REMARK 465 LEU B 9 REMARK 465 PRO B 10 REMARK 465 CYS B 11 REMARK 465 ASP B 12 REMARK 465 PRO B 13 REMARK 465 ALA B 14 REMARK 465 ARG B 15 REMARK 465 SER B 16 REMARK 465 HIS B 17 REMARK 465 PRO B 18 REMARK 465 THR B 19 REMARK 465 PRO B 20 REMARK 465 GLU B 21 REMARK 465 PHE B 22 REMARK 465 PRO B 23 REMARK 465 SER B 24 REMARK 465 SER B 25 REMARK 465 LEU B 26 REMARK 465 GLN B 27 REMARK 465 ASP B 28 REMARK 465 TYR B 29 REMARK 465 CYS B 30 REMARK 465 GLU B 31 REMARK 465 ILE B 32 REMARK 465 ARG B 33 REMARK 465 GLY B 34 REMARK 465 ILE B 35 REMARK 465 GLN B 36 REMARK 465 SER B 37 REMARK 465 GLN B 38 REMARK 465 PRO B 39 REMARK 465 PRO B 40 REMARK 465 ALA B 41 REMARK 465 ARG B 42 REMARK 465 ARG B 43 REMARK 465 ASP B 44 REMARK 465 PRO B 45 REMARK 465 THR B 46 REMARK 465 MET B 47 REMARK 465 ASP B 48 REMARK 465 TRP B 49 REMARK 465 LEU B 50 REMARK 465 ALA B 51 REMARK 465 SER B 52 REMARK 465 LEU B 53 REMARK 465 ARG B 54 REMARK 465 SER B 55 REMARK 465 GLN B 56 REMARK 465 ILE B 57 REMARK 465 LYS B 58 REMARK 465 PRO B 59 REMARK 465 HIS B 509 REMARK 465 HIS B 510 REMARK 465 HIS B 511 REMARK 465 HIS B 512 REMARK 465 HIS B 513 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 ALA A 103 -55.06 59.48 REMARK 500 HIS A 106 -84.53 -98.97 REMARK 500 ALA A 275 41.07 -108.74 REMARK 500 ASP A 296 -151.65 -109.18 REMARK 500 LLP A 311 -110.69 -97.40 REMARK 500 PRO A 396 20.22 -66.34 REMARK 500 TRP A 406 -17.58 -153.86 REMARK 500 ALA A 475 85.98 -150.50 REMARK 500 ARG B 61 -48.30 -25.95 REMARK 500 ALA B 103 -55.89 63.30 REMARK 500 HIS B 106 -61.13 -102.00 REMARK 500 HIS B 129 71.28 -114.49 REMARK 500 TRP B 133 71.63 -115.47 REMARK 500 ASP B 296 -149.68 -100.32 REMARK 500 LLP B 311 -108.82 -75.35 REMARK 500 THR B 349 -159.30 -118.76 REMARK 500 TRP B 406 -10.27 -154.99 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 B 767 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B 768 DISTANCE = 6.17 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5S5 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5S5 B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EUD RELATED DB: PDB DBREF 5EUE A 2 507 UNP Q67PY4 Q67PY4_SYMTH 2 507 DBREF 5EUE B 2 507 UNP Q67PY4 Q67PY4_SYMTH 2 507 SEQADV 5EUE MET A 0 UNP Q67PY4 INITIATING METHIONINE SEQADV 5EUE PRO A 1 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE PHE A 249 UNP Q67PY4 TYR 249 ENGINEERED MUTATION SEQADV 5EUE ILE A 344 UNP Q67PY4 LEU 344 ENGINEERED MUTATION SEQADV 5EUE ALA A 346 UNP Q67PY4 PHE 346 ENGINEERED MUTATION SEQADV 5EUE SER A 497 UNP Q67PY4 LEU 497 ENGINEERED MUTATION SEQADV 5EUE HIS A 508 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS A 509 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS A 510 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS A 511 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS A 512 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS A 513 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE MET B 0 UNP Q67PY4 INITIATING METHIONINE SEQADV 5EUE PRO B 1 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE PHE B 249 UNP Q67PY4 TYR 249 ENGINEERED MUTATION SEQADV 5EUE ILE B 344 UNP Q67PY4 LEU 344 ENGINEERED MUTATION SEQADV 5EUE ALA B 346 UNP Q67PY4 PHE 346 ENGINEERED MUTATION SEQADV 5EUE SER B 497 UNP Q67PY4 LEU 497 ENGINEERED MUTATION SEQADV 5EUE HIS B 508 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS B 509 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS B 510 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS B 511 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS B 512 UNP Q67PY4 EXPRESSION TAG SEQADV 5EUE HIS B 513 UNP Q67PY4 EXPRESSION TAG SEQRES 1 A 514 MET PRO LEU SER ALA PHE SER PRO PRO LEU PRO CYS ASP SEQRES 2 A 514 PRO ALA ARG SER HIS PRO THR PRO GLU PHE PRO SER SER SEQRES 3 A 514 LEU GLN ASP TYR CYS GLU ILE ARG GLY ILE GLN SER GLN SEQRES 4 A 514 PRO PRO ALA ARG ARG ASP PRO THR MET ASP TRP LEU ALA SEQRES 5 A 514 SER LEU ARG SER GLN ILE LYS PRO TYR ARG ASP ARG PHE SEQRES 6 A 514 PRO SER HIS ALA ARG LEU PRO ARG ALA GLY LEU PRO ARG SEQRES 7 A 514 ALA GLU ILE LEU ALA GLU ILE ALA ALA MET GLY ALA ALA SEQRES 8 A 514 GLU SER PRO ALA TRP ARG ASP GLY TYR ALA SER GLY ALA SEQRES 9 A 514 VAL TYR HIS GLY ASP GLU HIS HIS ILE ALA PHE LEU ASN SEQRES 10 A 514 GLU VAL TYR ALA LEU GLN SER GLN SER ASN PRO LEU HIS SEQRES 11 A 514 PRO ASP LEU TRP PRO SER THR ALA LYS PHE GLU ALA GLU SEQRES 12 A 514 VAL VAL ALA MET THR ALA HIS MET LEU GLY GLY ASP ALA SEQRES 13 A 514 ALA GLY GLY THR VAL CYS GLY THR VAL THR SER GLY GLY SEQRES 14 A 514 THR GLU SER LEU LEU LEU ALA MET LYS THR TYR ARG ASP SEQRES 15 A 514 TRP ALA ARG ALA THR LYS GLY ILE THR ALA PRO GLU ALA SEQRES 16 A 514 VAL VAL PRO VAL SER ALA HIS ALA ALA PHE ASP LYS ALA SEQRES 17 A 514 ALA GLN TYR PHE GLY ILE LYS LEU VAL ARG THR PRO LEU SEQRES 18 A 514 ASP ALA ASP TYR ARG ALA ASP VAL ALA ALA MET ARG GLU SEQRES 19 A 514 ALA ILE THR PRO ASN THR VAL VAL VAL ALA GLY SER ALA SEQRES 20 A 514 PRO GLY PHE PRO HIS GLY VAL VAL ASP PRO ILE PRO GLU SEQRES 21 A 514 ILE ALA ALA LEU ALA ALA GLU HIS GLY ILE GLY CYS HIS SEQRES 22 A 514 VAL ASP ALA CYS LEU GLY GLY PHE ILE LEU PRO TRP ALA SEQRES 23 A 514 GLU ARG LEU GLY TYR PRO VAL PRO PRO PHE ASP PHE ARG SEQRES 24 A 514 LEU GLU GLY VAL THR SER VAL SER ALA ASP THR HIS LLP SEQRES 25 A 514 TYR GLY TYR GLY ALA LYS GLY THR SER VAL ILE LEU TYR SEQRES 26 A 514 ARG ARG PRO ASP LEU LEU HIS TYR GLN TYR PHE ILE ALA SEQRES 27 A 514 ALA ASP TRP PRO GLY GLY ILE TYR ALA SER PRO THR PHE SEQRES 28 A 514 ALA GLY SER ARG PRO GLY ALA LEU SER ALA THR ALA TRP SEQRES 29 A 514 ALA ALA MET LEU SER LEU GLY GLU GLU GLY TYR LEU ASP SEQRES 30 A 514 ALA THR ARG ARG ILE LEU GLN ALA ALA ASP ARG LEU LYS SEQRES 31 A 514 ALA GLY VAL ARG ALA ILE PRO SER LEU LYS ILE LEU GLY SEQRES 32 A 514 ASP PRO LEU TRP VAL ILE ALA VAL ALA SER ASP GLU LEU SEQRES 33 A 514 ASN ILE TYR GLN VAL MET GLU GLU MET ALA GLY ARG GLY SEQRES 34 A 514 TRP ARG LEU ASN GLY LEU HIS ARG PRO PRO ALA PHE HIS SEQRES 35 A 514 VAL ALA LEU THR LEU ARG HIS THR GLU PRO GLY VAL VAL SEQRES 36 A 514 ASP ARG PHE LEU ALA ASP LEU GLN ASP ALA VAL ALA GLN SEQRES 37 A 514 VAL ARG ALA HIS PRO GLU LYS ALA THR GLY MET ALA PRO SEQRES 38 A 514 VAL TYR GLY MET ALA ALA ALA ALA PRO PRO GLU LEU VAL SEQRES 39 A 514 ARG GLN VAL SER THR GLY PHE ILE ASP LEU LEU TYR GLU SEQRES 40 A 514 VAL HIS HIS HIS HIS HIS HIS SEQRES 1 B 514 MET PRO LEU SER ALA PHE SER PRO PRO LEU PRO CYS ASP SEQRES 2 B 514 PRO ALA ARG SER HIS PRO THR PRO GLU PHE PRO SER SER SEQRES 3 B 514 LEU GLN ASP TYR CYS GLU ILE ARG GLY ILE GLN SER GLN SEQRES 4 B 514 PRO PRO ALA ARG ARG ASP PRO THR MET ASP TRP LEU ALA SEQRES 5 B 514 SER LEU ARG SER GLN ILE LYS PRO TYR ARG ASP ARG PHE SEQRES 6 B 514 PRO SER HIS ALA ARG LEU PRO ARG ALA GLY LEU PRO ARG SEQRES 7 B 514 ALA GLU ILE LEU ALA GLU ILE ALA ALA MET GLY ALA ALA SEQRES 8 B 514 GLU SER PRO ALA TRP ARG ASP GLY TYR ALA SER GLY ALA SEQRES 9 B 514 VAL TYR HIS GLY ASP GLU HIS HIS ILE ALA PHE LEU ASN SEQRES 10 B 514 GLU VAL TYR ALA LEU GLN SER GLN SER ASN PRO LEU HIS SEQRES 11 B 514 PRO ASP LEU TRP PRO SER THR ALA LYS PHE GLU ALA GLU SEQRES 12 B 514 VAL VAL ALA MET THR ALA HIS MET LEU GLY GLY ASP ALA SEQRES 13 B 514 ALA GLY GLY THR VAL CYS GLY THR VAL THR SER GLY GLY SEQRES 14 B 514 THR GLU SER LEU LEU LEU ALA MET LYS THR TYR ARG ASP SEQRES 15 B 514 TRP ALA ARG ALA THR LYS GLY ILE THR ALA PRO GLU ALA SEQRES 16 B 514 VAL VAL PRO VAL SER ALA HIS ALA ALA PHE ASP LYS ALA SEQRES 17 B 514 ALA GLN TYR PHE GLY ILE LYS LEU VAL ARG THR PRO LEU SEQRES 18 B 514 ASP ALA ASP TYR ARG ALA ASP VAL ALA ALA MET ARG GLU SEQRES 19 B 514 ALA ILE THR PRO ASN THR VAL VAL VAL ALA GLY SER ALA SEQRES 20 B 514 PRO GLY PHE PRO HIS GLY VAL VAL ASP PRO ILE PRO GLU SEQRES 21 B 514 ILE ALA ALA LEU ALA ALA GLU HIS GLY ILE GLY CYS HIS SEQRES 22 B 514 VAL ASP ALA CYS LEU GLY GLY PHE ILE LEU PRO TRP ALA SEQRES 23 B 514 GLU ARG LEU GLY TYR PRO VAL PRO PRO PHE ASP PHE ARG SEQRES 24 B 514 LEU GLU GLY VAL THR SER VAL SER ALA ASP THR HIS LLP SEQRES 25 B 514 TYR GLY TYR GLY ALA LYS GLY THR SER VAL ILE LEU TYR SEQRES 26 B 514 ARG ARG PRO ASP LEU LEU HIS TYR GLN TYR PHE ILE ALA SEQRES 27 B 514 ALA ASP TRP PRO GLY GLY ILE TYR ALA SER PRO THR PHE SEQRES 28 B 514 ALA GLY SER ARG PRO GLY ALA LEU SER ALA THR ALA TRP SEQRES 29 B 514 ALA ALA MET LEU SER LEU GLY GLU GLU GLY TYR LEU ASP SEQRES 30 B 514 ALA THR ARG ARG ILE LEU GLN ALA ALA ASP ARG LEU LYS SEQRES 31 B 514 ALA GLY VAL ARG ALA ILE PRO SER LEU LYS ILE LEU GLY SEQRES 32 B 514 ASP PRO LEU TRP VAL ILE ALA VAL ALA SER ASP GLU LEU SEQRES 33 B 514 ASN ILE TYR GLN VAL MET GLU GLU MET ALA GLY ARG GLY SEQRES 34 B 514 TRP ARG LEU ASN GLY LEU HIS ARG PRO PRO ALA PHE HIS SEQRES 35 B 514 VAL ALA LEU THR LEU ARG HIS THR GLU PRO GLY VAL VAL SEQRES 36 B 514 ASP ARG PHE LEU ALA ASP LEU GLN ASP ALA VAL ALA GLN SEQRES 37 B 514 VAL ARG ALA HIS PRO GLU LYS ALA THR GLY MET ALA PRO SEQRES 38 B 514 VAL TYR GLY MET ALA ALA ALA ALA PRO PRO GLU LEU VAL SEQRES 39 B 514 ARG GLN VAL SER THR GLY PHE ILE ASP LEU LEU TYR GLU SEQRES 40 B 514 VAL HIS HIS HIS HIS HIS HIS MODRES 5EUE LLP A 311 LYS MODIFIED RESIDUE MODRES 5EUE LLP B 311 LYS MODIFIED RESIDUE HET LLP A 311 24 HET LLP B 311 24 HET 5S5 A 601 29 HET PO4 A 602 5 HET PO4 B 601 5 HET 5S5 B 602 29 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 5S5 ~{N}-[(1~{S})-2-[(4-METHOXY-2,5-DIMETHYL-PHENYL) HETNAM 2 5S5 METHYLAMINO]-1-PHENYL-ETHYL]-5-METHYL-1,2-OXAZOLE-3- HETNAM 3 5S5 CARBOXAMIDE HETNAM PO4 PHOSPHATE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 5S5 2(C23 H27 N3 O3) FORMUL 4 PO4 2(O4 P 3-) FORMUL 7 HOH *126(H2 O) HELIX 1 AA1 PRO A 76 ASP A 97 1 22 HELIX 2 AA2 ASP A 108 GLN A 122 1 15 HELIX 3 AA3 TRP A 133 LEU A 151 1 19 HELIX 4 AA4 GLY A 167 GLY A 188 1 22 HELIX 5 AA5 ALA A 202 GLY A 212 1 11 HELIX 6 AA6 ASP A 227 ILE A 235 1 9 HELIX 7 AA7 PRO A 256 HIS A 267 1 12 HELIX 8 AA8 ILE A 281 LEU A 288 1 8 HELIX 9 AA9 ARG A 326 TYR A 332 1 7 HELIX 10 AB1 PRO A 355 ARG A 393 1 39 HELIX 11 AB2 ASN A 416 ARG A 427 1 12 HELIX 12 AB3 THR A 445 THR A 449 5 5 HELIX 13 AB4 GLY A 452 HIS A 471 1 20 HELIX 14 AB5 MET A 478 ALA A 487 1 10 HELIX 15 AB6 PRO A 489 GLU A 506 1 18 HELIX 16 AB7 PRO B 76 ASP B 97 1 22 HELIX 17 AB8 ASP B 108 SER B 123 1 16 HELIX 18 AB9 TRP B 133 LEU B 151 1 19 HELIX 19 AC1 GLY B 167 GLY B 188 1 22 HELIX 20 AC2 ALA B 202 GLY B 212 1 11 HELIX 21 AC3 ASP B 227 ILE B 235 1 9 HELIX 22 AC4 PRO B 256 GLY B 268 1 13 HELIX 23 AC5 ILE B 281 LEU B 288 1 8 HELIX 24 AC6 ARG B 326 HIS B 331 1 6 HELIX 25 AC7 PRO B 355 ALA B 394 1 40 HELIX 26 AC8 ASN B 416 GLY B 428 1 13 HELIX 27 AC9 THR B 445 GLU B 450 5 6 HELIX 28 AD1 GLY B 452 HIS B 471 1 20 HELIX 29 AD2 MET B 478 ALA B 488 1 11 HELIX 30 AD3 PRO B 489 TYR B 505 1 17 SHEET 1 AA1 7 CYS A 161 THR A 165 0 SHEET 2 AA1 7 SER A 320 TYR A 324 -1 O TYR A 324 N CYS A 161 SHEET 3 AA1 7 SER A 304 ALA A 307 -1 N VAL A 305 O LEU A 323 SHEET 4 AA1 7 GLY A 270 ASP A 274 1 N VAL A 273 O SER A 304 SHEET 5 AA1 7 THR A 239 SER A 245 1 N GLY A 244 O ASP A 274 SHEET 6 AA1 7 GLU A 193 PRO A 197 1 N GLU A 193 O VAL A 240 SHEET 7 AA1 7 LYS A 214 THR A 218 1 O VAL A 216 N ALA A 194 SHEET 1 AA2 2 PHE A 335 ALA A 337 0 SHEET 2 AA2 2 TYR A 345 SER A 347 -1 O TYR A 345 N ALA A 337 SHEET 1 AA3 4 LYS A 399 ILE A 400 0 SHEET 2 AA3 4 VAL A 407 ALA A 411 -1 O ALA A 411 N LYS A 399 SHEET 3 AA3 4 ALA A 439 ALA A 443 -1 O PHE A 440 N VAL A 410 SHEET 4 AA3 4 ASN A 432 LEU A 434 -1 N LEU A 434 O ALA A 439 SHEET 1 AA4 7 CYS B 161 THR B 165 0 SHEET 2 AA4 7 SER B 320 TYR B 324 -1 O TYR B 324 N CYS B 161 SHEET 3 AA4 7 SER B 304 ALA B 307 -1 N ALA B 307 O VAL B 321 SHEET 4 AA4 7 GLY B 270 ASP B 274 1 N VAL B 273 O SER B 304 SHEET 5 AA4 7 THR B 239 SER B 245 1 N GLY B 244 O ASP B 274 SHEET 6 AA4 7 GLU B 193 PRO B 197 1 N GLU B 193 O VAL B 240 SHEET 7 AA4 7 LYS B 214 THR B 218 1 O LYS B 214 N ALA B 194 SHEET 1 AA5 2 PHE B 335 ALA B 337 0 SHEET 2 AA5 2 TYR B 345 SER B 347 -1 O TYR B 345 N ALA B 337 SHEET 1 AA6 4 LYS B 399 ILE B 400 0 SHEET 2 AA6 4 VAL B 407 ALA B 411 -1 O ALA B 411 N LYS B 399 SHEET 3 AA6 4 ALA B 439 ALA B 443 -1 O VAL B 442 N ILE B 408 SHEET 4 AA6 4 ASN B 432 LEU B 434 -1 N LEU B 434 O ALA B 439 LINK C HIS A 310 N LLP A 311 1555 1555 1.35 LINK C LLP A 311 N TYR A 312 1555 1555 1.36 LINK C HIS B 310 N LLP B 311 1555 1555 1.36 LINK C LLP B 311 N TYR B 312 1555 1555 1.37 CISPEP 1 ALA A 246 PRO A 247 0 -3.16 CISPEP 2 ARG A 436 PRO A 437 0 4.41 CISPEP 3 ALA B 246 PRO B 247 0 -3.71 CISPEP 4 ARG B 436 PRO B 437 0 2.54 SITE 1 AC1 11 PRO A 127 PRO A 130 TRP A 340 ILE A 344 SITE 2 AC1 11 TYR A 345 ALA A 346 PHE B 249 ASN B 432 SITE 3 AC1 11 VAL B 496 SER B 497 PHE B 500 SITE 1 AC2 5 ALA A 103 TYR A 105 LYS A 317 ASN B 126 SITE 2 AC2 5 HIS B 129 SITE 1 AC3 5 ASN A 126 HIS A 129 ALA B 103 TYR B 105 SITE 2 AC3 5 LLP B 311 SITE 1 AC4 10 PHE A 249 VAL A 496 PHE A 500 PRO B 127 SITE 2 AC4 10 LEU B 128 PRO B 130 TRP B 340 ILE B 344 SITE 3 AC4 10 TYR B 345 ALA B 346 CRYST1 85.014 129.606 84.287 90.00 90.00 90.00 P 21 21 21 8 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 0.011763 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011864 0.00000