HEADER LIGASE 20-JAN-11 2Y67 TITLE NEW 5-BENZYLIDENETHIAZOLIDINE-4-ONE INHIBITORS OF BACTERIAL MURD TITLE 2 LIGASE: DESIGN, SYNTHESIS, CRYSTAL STRUCTURES, AND BIOLOGICAL TITLE 3 EVALUATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MURD LIGASE, D-GLUTAMIC ACID-ADDING ENZYME, UDP-N- COMPND 5 ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE; COMPND 6 EC: 6.3.2.9; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5[ALPHA]; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PABD16/MURD KEYWDS ATP-BINDING, CELL CYCLE, CELL DIVISION, CELL SHAPE, CELL WALL, CELL KEYWDS 2 WALL BIOGENESIS/DEGRADATION, LIGASE, NUCLEOTIDE-BINDING, KEYWDS 3 PEPTIDOGLYCAN SYNTHESIS, UMA EXPDTA X-RAY DIFFRACTION AUTHOR N.ZIDAR,T.TOMASIC,R.SINK,A.KOVAC,D.PATIN,D.BLANOT,C.CONTRERAS-MARTEL, AUTHOR 2 A.DESSEN,M.MULLER-PREMRU,A.ZEGA,S.GOBEC,L.PETERLIN-MASIC,D.KIKELJ REVDAT 3 20-DEC-23 2Y67 1 REMARK LINK REVDAT 2 02-NOV-11 2Y67 1 JRNL REVDAT 1 19-OCT-11 2Y67 0 JRNL AUTH N.ZIDAR,T.TOMASIC,R.SINK,A.KOVAC,D.PATIN,D.BLANOT, JRNL AUTH 2 C.CONTRERAS-MARTEL,A.DESSEN,M.M.PREMRU,A.ZEGA,S.GOBEC, JRNL AUTH 3 L.P.MASIC,D.KIKELJ JRNL TITL NEW 5-BENZYLIDENETHIAZOLIDIN-4-ONE INHIBITORS OF BACTERIAL JRNL TITL 2 MURD LIGASE: DESIGN, SYNTHESIS, CRYSTAL STRUCTURES, AND JRNL TITL 3 BIOLOGICAL EVALUATION. JRNL REF EUR.J.MED.CHEM V. 46 5512 2011 JRNL REFN ISSN 0223-5234 JRNL PMID 21963114 JRNL DOI 10.1016/J.EJMECH.2011.09.017 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 40963 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4601 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2235 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4800 REMARK 3 BIN FREE R VALUE SET COUNT : 259 REMARK 3 BIN FREE R VALUE : 0.4840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -1.60000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.146 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3411 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4641 ; 1.378 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 447 ; 7.274 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;34.568 ;24.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 563 ;16.278 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.831 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 534 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2586 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2178 ; 1.647 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3483 ; 2.508 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1233 ; 4.156 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1151 ; 6.098 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): 59.3872 -3.0995 14.6877 REMARK 3 T TENSOR REMARK 3 T11: 0.0687 T22: 0.0449 REMARK 3 T33: 0.0522 T12: 0.0109 REMARK 3 T13: -0.0231 T23: 0.0358 REMARK 3 L TENSOR REMARK 3 L11: 1.5739 L22: 2.1574 REMARK 3 L33: 4.1841 L12: -0.9694 REMARK 3 L13: 1.7026 L23: -0.0223 REMARK 3 S TENSOR REMARK 3 S11: 0.2041 S12: -0.0675 S13: -0.1547 REMARK 3 S21: -0.0993 S22: -0.0062 S23: 0.1317 REMARK 3 S31: 0.4977 S32: -0.0131 S33: -0.1978 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 94 A 295 REMARK 3 ORIGIN FOR THE GROUP (A): 37.3529 13.4381 4.0095 REMARK 3 T TENSOR REMARK 3 T11: 0.0694 T22: 0.0463 REMARK 3 T33: 0.0862 T12: -0.0020 REMARK 3 T13: -0.0421 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.0618 L22: 0.1996 REMARK 3 L33: 1.0104 L12: -0.1189 REMARK 3 L13: 0.7256 L23: -0.2695 REMARK 3 S TENSOR REMARK 3 S11: -0.0640 S12: -0.0504 S13: 0.1757 REMARK 3 S21: -0.0538 S22: 0.0064 S23: 0.0139 REMARK 3 S31: -0.0741 S32: -0.0685 S33: 0.0576 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 304 A 439 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1284 3.2845 26.2307 REMARK 3 T TENSOR REMARK 3 T11: 0.0187 T22: 0.0968 REMARK 3 T33: 0.0300 T12: 0.0076 REMARK 3 T13: -0.0168 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 3.1076 L22: 1.2646 REMARK 3 L33: 1.4215 L12: 0.1589 REMARK 3 L13: 0.0364 L23: 0.1689 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: -0.2828 S13: -0.0311 REMARK 3 S21: -0.0078 S22: -0.0346 S23: 0.0294 REMARK 3 S31: 0.0758 S32: -0.1166 S33: 0.0516 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 2Y67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290047056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97238 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD 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) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 46.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 33.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45000 REMARK 200 FOR SHELL : 3.060 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: PDB ENTRY 1UAG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6.0 MG/ML MURD, 20 MM HEPES PH 7.4, REMARK 280 200MM NACL, 5MM DITHIOTHREITOL, 0.05% (W/V) NAN3, 0.1M HEPES PH REMARK 280 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.35350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.67675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.03025 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ARG A 221 REMARK 465 GLY A 222 REMARK 465 ALA A 223 REMARK 465 ASP A 224 REMARK 465 HIS A 440 REMARK 465 HIS A 441 REMARK 465 HIS A 442 REMARK 465 HIS A 443 REMARK 465 HIS A 444 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 LEU A 13 -122.28 -94.25 REMARK 500 SER A 56 174.59 179.43 REMARK 500 PHE A 303 65.39 33.54 REMARK 500 ASP A 317 41.79 -109.40 REMARK 500 ARG A 357 -32.33 -39.07 REMARK 500 ARG A 380 84.84 -161.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 175 ILE A 176 149.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N21 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1440 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UUO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2JFG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP REMARK 900 RELATED ID: 4UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 3UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 1E0D RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2VTE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2JFF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 1EEH RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2X5O RELATED DB: PDB REMARK 900 DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE- AND 5-BENZYLIDENE- REMARK 900 THIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD LIGASE REMARK 900 RELATED ID: 2WJP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 RHODANINE INHIBITOR REMARK 900 RELATED ID: 2VTD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2Y1O RELATED DB: PDB REMARK 900 DUAL-TARGET INHIBITOR OF MURD AND MURE LIGASES: DESIGN, SYNTHESIS REMARK 900 AND BINDING MODE STUDIES REMARK 900 RELATED ID: 1UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2JFH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH L-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2UUP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2Y66 RELATED DB: PDB REMARK 900 NEW 5-BENZYLIDENETHIAZOLIDINE-4-ONE INHIBITORS OF BACTERIAL MURD REMARK 900 LIGASE: DESIGN, SYNTHESIS CRYSTAL STRUCTURES, AND BIOLOGICAL REMARK 900 EVALUATION, REMARK 900 RELATED ID: 2Y68 RELATED DB: PDB REMARK 900 STRUCTURE-BASED DESIGN OF A NEW SERIES OF D-GLUTAMIC ACID-BASED REMARK 900 INHIBITORS OF BACTERIAL MURD LIGASE DBREF 2Y67 A 0 437 UNP P14900 MURD_ECOLI 1 438 SEQADV 2Y67 SER A 438 UNP P14900 EXPRESSION TAG SEQADV 2Y67 HIS A 439 UNP P14900 EXPRESSION TAG SEQADV 2Y67 HIS A 440 UNP P14900 EXPRESSION TAG SEQADV 2Y67 HIS A 441 UNP P14900 EXPRESSION TAG SEQADV 2Y67 HIS A 442 UNP P14900 EXPRESSION TAG SEQADV 2Y67 HIS A 443 UNP P14900 EXPRESSION TAG SEQADV 2Y67 HIS A 444 UNP P14900 EXPRESSION TAG SEQRES 1 A 445 MET ALA ASP TYR GLN GLY LYS ASN VAL VAL ILE ILE GLY SEQRES 2 A 445 LEU GLY LEU THR GLY LEU SER CYS VAL ASP PHE PHE LEU SEQRES 3 A 445 ALA ARG GLY VAL THR PRO ARG VAL MET ASP THR ARG MET SEQRES 4 A 445 THR PRO PRO GLY LEU ASP LYS LEU PRO GLU ALA VAL GLU SEQRES 5 A 445 ARG HIS THR GLY SER LEU ASN ASP GLU TRP LEU MET ALA SEQRES 6 A 445 ALA ASP LEU ILE VAL ALA SER PRO GLY ILE ALA LEU ALA SEQRES 7 A 445 HIS PRO SER LEU SER ALA ALA ALA ASP ALA GLY ILE GLU SEQRES 8 A 445 ILE VAL GLY ASP ILE GLU LEU PHE CYS ARG GLU ALA GLN SEQRES 9 A 445 ALA PRO ILE VAL ALA ILE THR GLY SER ASN GLY LYS SER SEQRES 10 A 445 THR VAL THR THR LEU VAL GLY GLU MET ALA LYS ALA ALA SEQRES 11 A 445 GLY VAL ASN VAL GLY VAL GLY GLY ASN ILE GLY LEU PRO SEQRES 12 A 445 ALA LEU MET LEU LEU ASP ASP GLU CYS GLU LEU TYR VAL SEQRES 13 A 445 LEU GLU LEU SER SER PHE GLN LEU GLU THR THR SER SER SEQRES 14 A 445 LEU GLN ALA VAL ALA ALA THR ILE LEU ASN VAL THR GLU SEQRES 15 A 445 ASP HIS MET ASP ARG TYR PRO PHE GLY LEU GLN GLN TYR SEQRES 16 A 445 ARG ALA ALA KCX LEU ARG ILE TYR GLU ASN ALA LYS VAL SEQRES 17 A 445 CYS VAL VAL ASN ALA ASP ASP ALA LEU THR MET PRO ILE SEQRES 18 A 445 ARG GLY ALA ASP GLU ARG CYS VAL SER PHE GLY VAL ASN SEQRES 19 A 445 MET GLY ASP TYR HIS LEU ASN HIS GLN GLN GLY GLU THR SEQRES 20 A 445 TRP LEU ARG VAL LYS GLY GLU LYS VAL LEU ASN VAL LYS SEQRES 21 A 445 GLU MET LYS LEU SER GLY GLN HIS ASN TYR THR ASN ALA SEQRES 22 A 445 LEU ALA ALA LEU ALA LEU ALA ASP ALA ALA GLY LEU PRO SEQRES 23 A 445 ARG ALA SER SER LEU LYS ALA LEU THR THR PHE THR GLY SEQRES 24 A 445 LEU PRO HIS ARG PHE GLU VAL VAL LEU GLU HIS ASN GLY SEQRES 25 A 445 VAL ARG TRP ILE ASN ASP SER LYS ALA THR ASN VAL GLY SEQRES 26 A 445 SER THR GLU ALA ALA LEU ASN GLY LEU HIS VAL ASP GLY SEQRES 27 A 445 THR LEU HIS LEU LEU LEU GLY GLY ASP GLY LYS SER ALA SEQRES 28 A 445 ASP PHE SER PRO LEU ALA ARG TYR LEU ASN GLY ASP ASN SEQRES 29 A 445 VAL ARG LEU TYR CYS PHE GLY ARG ASP GLY ALA GLN LEU SEQRES 30 A 445 ALA ALA LEU ARG PRO GLU VAL ALA GLU GLN THR GLU THR SEQRES 31 A 445 MET GLU GLN ALA MET ARG LEU LEU ALA PRO ARG VAL GLN SEQRES 32 A 445 PRO GLY ASP MET VAL LEU LEU SER PRO ALA CYS ALA SER SEQRES 33 A 445 LEU ASP GLN PHE LYS ASN PHE GLU GLN ARG GLY ASN GLU SEQRES 34 A 445 PHE ALA ARG LEU ALA LYS GLU LEU GLY SER HIS HIS HIS SEQRES 35 A 445 HIS HIS HIS MODRES 2Y67 KCX A 198 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 198 12 HET N21 A 500 35 HET SO4 A1440 5 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM N21 (2R)-2-[[4-[[4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5- HETNAM 2 N21 YLIDENE)METHYL]PHENOXY]METHYL]PHENYL]SULFONYLAMINO]PEN HETNAM 3 N21 TANEDIOIC ACID HETNAM SO4 SULFATE ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 N21 C22 H20 N2 O9 S2 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *221(H2 O) HELIX 1 1 LEU A 13 ALA A 26 1 14 HELIX 2 2 GLY A 42 LEU A 46 5 5 HELIX 3 3 ASN A 58 ALA A 65 1 8 HELIX 4 4 HIS A 78 ALA A 87 1 10 HELIX 5 5 GLY A 93 ALA A 102 1 10 HELIX 6 6 GLY A 114 ALA A 129 1 16 HELIX 7 7 PRO A 142 LEU A 147 1 6 HELIX 8 8 SER A 159 THR A 165 1 7 HELIX 9 9 HIS A 183 TYR A 187 5 5 HELIX 10 10 PHE A 189 ARG A 200 1 12 HELIX 11 11 ILE A 201 GLU A 203 5 3 HELIX 12 12 ASP A 214 MET A 218 5 5 HELIX 13 13 LYS A 259 MET A 261 5 3 HELIX 14 14 GLY A 265 ALA A 282 1 18 HELIX 15 15 PRO A 285 PHE A 296 1 12 HELIX 16 16 ASN A 322 ASN A 331 1 10 HELIX 17 17 PHE A 352 LEU A 359 5 8 HELIX 18 18 ASP A 372 ALA A 378 1 7 HELIX 19 19 LEU A 379 GLU A 382 5 4 HELIX 20 20 THR A 389 ALA A 398 1 10 HELIX 21 21 PRO A 399 VAL A 401 5 3 HELIX 22 22 ASN A 421 GLY A 437 1 17 SHEET 1 AA 5 ARG A 52 THR A 54 0 SHEET 2 AA 5 ARG A 32 ASP A 35 1 O VAL A 33 N HIS A 53 SHEET 3 AA 5 VAL A 8 ILE A 11 1 O VAL A 8 N ARG A 32 SHEET 4 AA 5 LEU A 67 ALA A 70 1 O LEU A 67 N VAL A 9 SHEET 5 AA 5 GLU A 90 VAL A 92 1 O GLU A 90 N ILE A 68 SHEET 1 AB 6 VAL A 133 GLY A 137 0 SHEET 2 AB 6 LEU A 153 GLU A 157 1 O LEU A 153 N GLY A 134 SHEET 3 AB 6 ILE A 106 THR A 110 1 O VAL A 107 N LEU A 156 SHEET 4 AB 6 ALA A 173 ILE A 176 1 O ALA A 173 N ALA A 108 SHEET 5 AB 6 CYS A 208 ASN A 211 1 O VAL A 209 N ILE A 176 SHEET 6 AB 6 VAL A 228 PHE A 230 1 O VAL A 228 N VAL A 210 SHEET 1 AC 3 TYR A 237 GLN A 242 0 SHEET 2 AC 3 GLU A 245 VAL A 250 -1 O GLU A 245 N GLN A 242 SHEET 3 AC 3 GLU A 253 ASN A 257 -1 O GLU A 253 N VAL A 250 SHEET 1 AD 6 GLU A 304 HIS A 309 0 SHEET 2 AD 6 VAL A 312 ASN A 316 -1 O VAL A 312 N HIS A 309 SHEET 3 AD 6 MET A 406 LEU A 409 1 O VAL A 407 N ILE A 315 SHEET 4 AD 6 LEU A 339 GLY A 344 1 O HIS A 340 N LEU A 408 SHEET 5 AD 6 VAL A 364 PHE A 369 1 O ARG A 365 N LEU A 341 SHEET 6 AD 6 ALA A 384 GLN A 386 1 O GLU A 385 N CYS A 368 SSBOND 1 CYS A 208 CYS A 227 1555 1555 2.05 LINK C ALA A 197 N KCX A 198 1555 1555 1.33 LINK C KCX A 198 N LEU A 199 1555 1555 1.34 SITE 1 AC1 15 ILE A 11 GLY A 12 ASP A 35 THR A 36 SITE 2 AC1 15 ARG A 37 SER A 71 PHE A 161 HIS A 183 SITE 3 AC1 15 LYS A 348 ALA A 414 SER A 415 ASN A 421 SITE 4 AC1 15 PHE A 422 HOH A2088 HOH A2174 SITE 1 AC2 7 ASN A 113 GLY A 114 LYS A 115 SER A 116 SITE 2 AC2 7 THR A 117 ARG A 302 HOH A2068 CRYST1 65.326 65.326 134.707 90.00 90.00 90.00 P 41 4 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 0.015308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007424 0.00000