Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  R195K E. COLI MENE WITH BOUND OSB-AMS
 
Authors :  J. S. Matarlo, R. Shek, K. R. Rajashankar, P. J. Tonge, J. B. French
Date :  19 Jun 15  (Deposition) - 07 Oct 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Matarlo, C. E. Evans, I. Sharma, L. J. Lavaud, S. C. Ngo, R. Shek, K. R. Rajashankar, J. B. French, D. S. Tan, P. J. Tonge
Mechanism Of Mene Inhibition By Acyl-Adenylate Analogues An Discovery Of Novel Antibacterial Agents.
Biochemistry V. 54 6514 2015
PubMed-ID: 26394156  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00966

(-) Compounds

Molecule 1 - 2-SUCCINYLBENZOATE--COA LIGASE
    Chains: A, B
    EC Number: 6.2.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MENE, B2260, JW2255
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: O-SUCCINYLBENZOYL-COA SYNTHETASE,OSB-COA SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
14YB2Ligand/Ion5'-O-{[4-(2-CARBOXYPHENYL)-4-OXOBUTANOYL]SULFAMOYL}ADENOSINE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14YB1Ligand/Ion5'-O-{[4-(2-CARBOXYPHENYL)-4-OXOBUTANOYL]SULFAMOYL}ADENOSINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14YB1Ligand/Ion5'-O-{[4-(2-CARBOXYPHENYL)-4-OXOBUTANOYL]SULFAMOYL}ADENOSINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:9 , CYS A:34 , ASP A:38 , GLN A:74binding site for residue MG A 501
2AC2SOFTWARESER A:188 , LEU A:223 , LEU A:244 , LEU A:245 , GLY A:246 , GLY A:247 , ALA A:248 , ALA A:249 , GLY A:268 , TYR A:269 , GLY A:270 , LEU A:271 , THR A:272 , SER A:276 , THR A:277 , ASP A:336 , ILE A:347 , ARG A:350 , LYS A:437 , HOH A:605 , HOH A:614 , HOH A:623 , HOH A:661 , HOH A:666 , HOH A:677binding site for residue 4YB A 502
3AC3SOFTWAREGLN A:132 , PRO A:133 , THR A:134 , HOH A:602 , GLY B:48binding site for residue MG B 501
4AC4SOFTWAREASN B:61 , PRO B:183 , HOH B:721binding site for residue MG B 502
5AC5SOFTWARELEU B:182 , HIS B:186 , SER B:188 , LEU B:223 , LEU B:244 , LEU B:245 , GLY B:246 , GLY B:247 , ALA B:248 , ALA B:249 , GLY B:268 , TYR B:269 , GLY B:270 , LEU B:271 , THR B:272 , SER B:276 , THR B:277 , VAL B:289 , ASP B:336 , ARG B:350 , LYS B:437 , HOH B:606 , HOH B:630 , HOH B:654 , HOH B:663 , HOH B:672binding site for residue 4YB B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C5H)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:124 -Gly A:125
2Glu B:124 -Gly B:125
3Asp B:174 -His B:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C5H)

(-) Exons   (0, 0)

(no "Exon" information available for 5C5H)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh...eee...........eee.................eeeeee........eeeeehhhhhhhhhhhhh........eee......hhhhhhhhhhhhhhh.eeee....hhhhhh....eeeehhhhhhhhhhhh......eeee.....hhhhhhhhhhh...eeeeeeehhhheeeeeee........ee...eeeeee..eeeeee.....eeee..eee........eeeeeeeeee..eeeeeee.hhheee..eeehhhhhhhhhh....eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhh...eee.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c5h A  -1 SHMIFSDWPWRHWRQVRGETIALRLNDEQLNWRELCARVDELASGFAVQGVVEGSGVMLRAWNTPQTLLAWLALLQCGARVLPVNPQLPQPLLEELLPNLTLQFALVPDGENTFPALTSLHIQLVEGAHAATWQPTRLCSMTLTSSTGLPKAAVHTYQAHLASAQGVLSLIPFGDHDDWLLSLPLFHVSGQGIMWKWLYAGARMTVRDKQPLEQMLAGCTHASLVPTQLWRLLVNRSSVSLKAVLLGGAAIPVELTEQAREQGIRCFCGYGLTEFASTVCAKEADGLADVGSPLPGREVKIVNNEVWLRAASMAEGYWRNGQLVSLVNDEGWYATRDRGEMHNGKLTIVGRLDNLFFSGGEGIQPEEVERVIAAHPAVLQVFIVPVADKFGHRPVAVMEYDHESVDLSEWVKDKLARFQQPVRWLTLPPKISRQALKEWVQRQ 450
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138    || 149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       390       400       410       420       437       447   
                                                                                                                                                                          143|                                                                                                                                                                                                                                                388|                                    429|             
                                                                                                                                                                           145                                                                                                                                                                                                                                                 390                                     437             


Chain B from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhh..eee...........eee.................eeeeee.......eeeeehhhhhhhhhhhhh........eee......hhhhhhhhhhhhhhh.eeee....hhhhhh....eeeehhhhhhhhhhh.......eeee.....hhhhhhhhhhh...eeeeeeehhhheeeeeee........ee...eeeeee..eeeeee.....eeee..eee........eeeeeeeeee..eeeeeee.hhheee..eeehhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee........hhhhhh.hhhhh...eee..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c5h B   0 HMIFSDWPWRHWRQVRGETIALRLNDEQLNWRELCARVDELASGFAVQGVVEGSGVMLRAWNTPQTLLAWLALLQCGARVLPVNPQLPQPLLEELLPNLTLQFALVPDGENTFPALTSLHIQLVEGAHAATWQPTRLCSMTLTSGGLPKAAVHTYQAHLASAQGVLSLIPFGDHDDWLLSLPLFHVSGQGIMWKWLYAGARMTVRDKQPLEQMLAGCTHASLVPTQLWRLLVNRSSVSLKAVLLGGAAIPVELTEQAREQGIRCFCGYGLTEFASTVCAKEADGLADVGSPLPGREVKIVNNEVWLRAASMAEGYWRNGQLVSLVNDEGWYATRDRGEMHNGKLTIVGRLDNLFFSGGEGIQPEEVERVIAAHPAVLQVFIVPVADKEFGHRPVAVMEYDHESVDLSEWVKDKLARFQQPVRWLTLPPELKGIKISRQALKEWVQRQQ 451
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139    || 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431||     443        
                                                                                                                                                                          144|                                                                                                                                                                                                                                                                                          432|                
                                                                                                                                                                           147                                                                                                                                                                                                                                                                                           435
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5C5H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C5H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C5H)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4YB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp B:174 - His B:175   [ RasMol ]  
    Glu A:124 - Gly A:125   [ RasMol ]  
    Glu B:124 - Gly B:125   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5c5h
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MENE_ECOLI | P37353
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.2.1.26
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MENE_ECOLI | P37353
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 5C5H)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5C5H)