HEADER LIGASE 06-MAR-07 2UUP TITLE CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING TITLE 2 SULFONAMIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDP-N- ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE, D- COMPND 5 GLUTAMIC ACID- ADDING ENZYME, UDP-N-ACETYLMURAMOYL-L-ALANYL-D- COMPND 6 GLUTAMATE LIGASE; COMPND 7 EC: 6.3.2.9; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: INHIBITOR N-(6-(4-CYANO-BENZYLOXY)-NAPHTHALENE-2- COMPND 10 SULFONYL)-D-GLUTAMIC ACID BOUND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PABD16 KEYWDS MURD-INHIBITOR COMPLEX, PEPTIDOGLYCAN SYNTHESIS, LIGASE, CELL WALL, KEYWDS 2 CELL SHAPE, CELL CYCLE, NUCLEOTIDE-BINDING, SULFONAMIDE INHIBITOR, KEYWDS 3 MURD LIGASE, ATP-BINDING, CELL DIVISION EXPDTA X-RAY DIFFRACTION AUTHOR J.HUMLJAN,M.KOTNIK,C.CONTRERAS-MARTEL,D.BLANOT,U.URLEB,A.DESSEN, AUTHOR 2 T.SOLMAJER,S.GOBEC REVDAT 5 13-DEC-23 2UUP 1 LINK REVDAT 4 31-JAN-18 2UUP 1 SOURCE JRNL REVDAT 3 24-MAR-09 2UUP 1 JRNL REVDAT 2 24-FEB-09 2UUP 1 VERSN REVDAT 1 25-MAR-08 2UUP 0 JRNL AUTH J.HUMLJAN,M.KOTNIK,C.CONTRERAS-MARTEL,D.BLANOT,U.URLEB, JRNL AUTH 2 A.DESSEN,T.SOLMAJER,S.GOBEC JRNL TITL NOVEL NAPHTHALENE-N-SULFONYL-D-GLUTAMIC ACID DERIVATIVES AS JRNL TITL 2 INHIBITORS OF MURD, A KEY PEPTIDOGLYCAN BIOSYNTHESIS ENZYME. JRNL REF J. MED. CHEM. V. 51 7486 2008 JRNL REFN ISSN 1520-4804 JRNL PMID 19007109 JRNL DOI 10.1021/JM800762U REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 43882 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2303 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) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3165 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3305 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.06000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3416 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4643 ; 1.411 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 442 ; 5.986 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;32.809 ;24.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;12.096 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;15.943 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 531 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2586 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1588 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2302 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 340 ; 0.177 ; 0.200 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): 40 ; 0.157 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.227 ; 0.200 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): 2184 ; 0.855 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3485 ; 1.503 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1232 ; 2.270 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1156 ; 3.604 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: NULL REMARK 4 REMARK 4 2UUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1290031765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45633 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 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 3UAG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.7 M REMARK 280 (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 1 MM REMARK 280 INHIBITOR SOLUTION. 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 68.08700 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 34.04350 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 102.13050 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: PQS 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 HIS A 441 REMARK 465 HIS A 442 REMARK 465 HIS A 443 REMARK 465 HIS A 444 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 HIS A 440 CA C O CB CG ND1 CD2 REMARK 470 HIS A 440 CE1 NE2 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 O HOH A 2152 O HOH A 2318 1.73 REMARK 500 O HOH A 2054 O HOH A 2137 2.12 REMARK 500 O HOH A 2056 O HOH A 2057 2.16 REMARK 500 OE2 GLU A 245 O HOH A 2256 2.17 REMARK 500 O HOH A 2374 O HOH A 2402 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 LEU A 13 -118.89 -91.21 REMARK 500 ASP A 224 -161.79 -125.00 REMARK 500 GLN A 242 -124.36 -127.38 REMARK 500 GLN A 243 -84.50 -68.98 REMARK 500 PHE A 303 51.32 37.53 REMARK 500 ARG A 380 79.29 -160.53 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 A2035 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A2077 DISTANCE = 6.74 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LK4 A1440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1441 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1442 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1443 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E0D RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 1EEH RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 1UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE 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: 2JFG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP 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: 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: 4UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE 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 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL HIS-TAG (SHHHHHH) DBREF 2UUP A 0 0 PDB 2UUP 2UUP 0 0 DBREF 2UUP A 1 437 UNP P14900 MURD_ECOLI 1 437 DBREF 2UUP A 438 444 PDB 2UUP 2UUP 438 444 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 2UUP KCX A 198 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 198 12 HET LK4 A1440 33 HET SO4 A1441 5 HET SO4 A1442 5 HET SO4 A1443 5 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM LK4 N-({6-[(4-CYANOBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D- HETNAM 2 LK4 GLUTAMIC ACID HETNAM SO4 SULFATE ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 LK4 C23 H20 N2 O7 S FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *418(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 ARG A 100 1 8 HELIX 6 6 GLY A 114 ALA A 129 1 16 HELIX 7 7 PRO A 142 LEU A 147 5 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 CYS A 227 PHE A 230 1 O VAL A 228 N VAL A 210 SHEET 1 AC 3 TYR A 237 HIS A 241 0 SHEET 2 AC 3 THR A 246 VAL A 250 -1 O TRP A 247 N ASN A 240 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 1.34 LINK C KCX A 198 N LEU A 199 1555 1555 1.33 SITE 1 AC1 21 ILE A 11 GLY A 12 ASP A 35 THR A 36 SITE 2 AC1 21 ARG A 37 LEU A 57 SER A 71 GLY A 73 SITE 3 AC1 21 PHE A 161 HIS A 183 LYS A 348 ALA A 414 SITE 4 AC1 21 SER A 415 LEU A 416 ASN A 421 PHE A 422 SITE 5 AC1 21 HOH A2187 HOH A2412 HOH A2413 HOH A2414 SITE 6 AC1 21 HOH A2415 SITE 1 AC2 10 ASN A 113 GLY A 114 LYS A 115 SER A 116 SITE 2 AC2 10 THR A 117 ARG A 302 LYS A 319 HOH A2416 SITE 3 AC2 10 HOH A2417 HOH A2418 SITE 1 AC3 6 THR A 166 SER A 167 SER A 168 LEU A 169 SITE 2 AC3 6 ARG A 200 GLU A 203 SITE 1 AC4 5 HIS A 309 ASN A 310 SER A 438 HIS A 439 SITE 2 AC4 5 HIS A 440 CRYST1 65.517 65.517 136.174 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 0.015263 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007344 0.00000