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
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)

(-) Description

Title :  ENDURACIDIDINE BIOSYNTHESIS ENZYME MPPR COMPLEXED WITH PYRUVATE
 
Authors :  N. R. Silvaggi
Date :  13 Mar 13  (Deposition) - 03 Jul 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Acetoacetate Decarboxylase-Like, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Burroughs, R. W. Hoppe, N. C. Goebel, B. H. Sayyed, T. J. Voegtline A. W. Schwabacher, T. M. Zabriskie, N. R. Silvaggi
Structural And Functional Characterization Of Mppr, An Enduracididine Biosynthetic Enzyme From Streptomyces Hygroscopicus: Functional Diversity In The Acetoacetate Decarboxylase-Like Superfamily.
Biochemistry V. 52 4492 2013
PubMed-ID: 23758195  |  Reference-DOI: 10.1021/BI400397K

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN MPPR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PE-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MPPR
    Organism Scientific: STREPTOMYCES HYGROSCOPICUS
    Organism Taxid: 1912

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PYR3Ligand/IonPYRUVIC ACID
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1PYR6Ligand/IonPYRUVIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:116 , GLU A:118 , PRO A:145 , ARG A:148 , GLN A:152 , LYS A:156BINDING SITE FOR RESIDUE PYR A 401
2AC2SOFTWAREPHE B:116 , GLU B:118 , PRO B:145 , ARG B:148 , GLN B:152 , LYS B:156BINDING SITE FOR RESIDUE PYR B 401
3AC3SOFTWAREARG A:191 , ARG A:192 , HOH A:629 , ARG B:191 , ARG B:192 , HOH B:554BINDING SITE FOR RESIDUE PYR B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:40 -Pro A:41
2Pro A:54 -Pro A:55
3Leu B:40 -Pro B:41
4Pro B:54 -Pro B:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JMC)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeeeeeeeeee.hhhhhhhh.....ee.....eeeeeeeeeeeee..hhhhhhhhhheeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhh...eee.eeee.................eeeeeeee..eeeeeeeeeeeeee...hhhhh...eeee........eeeeeeeeeeee..eeeeeeeeee....hhhhhh....eeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jmc A  33 AGPVGYSLPLSPTGESAMLTPPPWHFSGEVVMVDYRVDPDAARRFLPPGLEPGADPGAAAAVFATWQWCSQDGAELTDPGRCQFGEFLILLSCEFEGRPMARCPYAWVDQAVPMMRGWVQGMPKQFGVIHQSRPVTVGKAGSRLAPGGRFDGALSVHGRRVVEASVTVDRSTDQPPALHDVPLAHTLVFPEWVRPRLVASEVSDVEFSPIWTGSGDLTFFDGLGDDFGALAPLEVGSGHVFSYGETLHGGRLLSDYS 295
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222  ||   238       248       258       268       278       288       
                                                                                                                                                                                                                          225|                                                               
                                                                                                                                                                                                                           232                                                               


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......................eeeeeeeeeeeee.hhhhhhh.....eee.....eeeeeeeeeeeee..hhhhhhhhhheeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhh...eee.eeee.................eeeeeeee..eeeeeeeeeeeeee...hhhhh...eeee..........eeeeeeeeeeee..eeeeeeeeee....hhhhhh....eeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jmc B  34 GPVGYSLPLSPTGESAMLTPPPWHFSGEVVMVDYRVDPDAARRFLPPGLEPGADPGAAAAVFATWQWCSQDGAELTDPGRCQFGEFLILLSCEFEGRPMARCPYAWVDQAVPMMRGWVQGMPKQFGVIHQSRPVTVGKAGSRLAPGGRFDGALSVHGRRVVEASVTVDRSTDQPPALHDVPLAHTLVFPEWVPPRPRLVASEVSDVEFSPIWTGSGDLTFFDGLGDDFGALAPLEVGSGHVFSYGETLHGGRLLSDYS 295
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  ||   237       247       257       267       277       287        
                                                                                                                                                                                                                          226|                                                                
                                                                                                                                                                                                                           231
   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 4JMC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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
    PYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:40 - Pro A:41   [ RasMol ]  
    Leu B:40 - Pro B:41   [ RasMol ]  
    Pro A:54 - Pro A:55   [ RasMol ]  
    Pro B:54 - Pro B:55   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4jmc
    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
  Q643B8_STRHY | Q643B8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q643B8_STRHY | Q643B8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q643B8_STRHY | Q643B8: 4jm3 4jmd 4jme

(-) Related Entries Specified in the PDB File

4jm3 4jmd 4jme