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

(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE--D-ALANINE LIGASE FROM BURKHOLDERIA AMBIFARIA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  30 Mar 12  (Deposition) - 09 May 12  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DDL, BAMMC406_0490
    Organism Scientific: BURKHOLDERIA AMBIFARIA
    Organism Taxid: 398577
    Strain: MC40-6
    Synonym: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:90 , GLY A:92 , HOH A:592BINDING SITE FOR RESIDUE EDO A 401
2AC2SOFTWAREGLU A:75 , ASN A:277 , ALA A:279BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREARG B:260 , PRO B:280 , GLY B:281 , SER B:286 , LEU B:287 , PRO B:288 , HOH B:588BINDING SITE FOR RESIDUE EDO B 401
4AC4SOFTWAREPRO B:235 , ALA B:236BINDING SITE FOR RESIDUE EDO B 402
5AC5SOFTWAREASP B:39BINDING SITE FOR RESIDUE EDO B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EG0)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Leu A:143 -Pro A:144
2Ile A:230 -Pro A:231
3Arg B:126 -Gly B:127
4Leu B:143 -Pro B:144
5Ile B:230 -Pro B:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EG0)

(-) Exons   (0, 0)

(no "Exon" information available for 4EG0)

(-) Sequences/Alignments

Asymmetric/Biological 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4eg0a1 A:4-102 automated matches                                                                  d4eg0a2 A:103-311 automated matches                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee....eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.......eeee..eee.....hhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eg0 A   4 IDPKRFGKVAVLFGGESAEREVSLTSGRLVLQGLRDAGIDAHPFDPAERPLSALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQTGVPTPPFETVMRGDDYAARATDIVAKLGLPLFVKPASAVLKVKTADALPAALSEAATHDKIVIVEKSIEGGGEYTACIAGDLDLPLIKIVPTQYLIPCGLPAEQETELKRIARRAFDVLGCTDWGRADFMLDAAGNAYFLEVNTAPGMTDHSLPPKAARSIGIGYSELVVKVLSLTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       158       168       178       188       198       208 ||    233       243       253       263       273       283       293       303        
                                                                                                                                                                             151|                                                  210|                                                                                     
                                                                                                                                                                              157                                                   226                                                                                     


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4eg0b1 B:4-102 automated matches                                                                  d4eg0b2 B:103-311 automated matches                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeee...hhhhh.hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee...eee.hhhhhhhhhhh....eeeeee.....eeeeeeee......eeeeehhhhh...eee.....hhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eg0 B   4 IDPKRFGKVAVLFGGESAEREVSLTSGRLVLQGLRDAGIDAHPFDPAERPLSALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQTGVPTPPFETVMRGDDYAARATDIVAKLGLPLFVKPASVLKVKTADALPAALSEAHDKIVIVEKSIEGGGEYTACIAGDLDLPLIKIVPAGEFYDTQYLIPCGLPAEQETELKRIARRAFDVLGCTDWGRADFMLDAAGNAYFLEVNTAPGMTDHSLPPKAARSIGIGYSELVVKVLSLTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       159       169    || 181       191       201       211   ||  230       240       250       260       270       280       290       300       310 
                                                                                                                                                                             151|             174|                                   215|                                                                                      
                                                                                                                                                                              158              177                                    225
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EG0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EG0)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    EDO  [ 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
    Arg B:126 - Gly B:127   [ RasMol ]  
    Ile A:230 - Pro A:231   [ RasMol ]  
    Ile B:230 - Pro B:231   [ RasMol ]  
    Leu A:143 - Pro A:144   [ RasMol ]  
    Leu B:143 - Pro B:144   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4eg0
    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
  DDL_BURA4 | B1YSS6
    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)
  6.3.2.4
    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
  DDL_BURA4 | B1YSS6
    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 4EG0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4EG0)