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

(-) Description

Title :  CRYSTAL STRUCTURE OF ISOPRENOID BIOSYNTHESIS PROTEIN WITH AMIDOTRANSFERASE-LIKE DOMAIN FROM EHRLICHIA CHAFFEENSIS AT 1.90A RESOLUTION
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  16 Dec 09  (Deposition) - 19 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Als Collaborative Crystallography, Ehrlichia Chaffeensis, Isoprenoid Biosynthesis, Amidotransferase-Like Domain, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, B. Sankaran, T. E. Edwards, B. Staker
Crystal Structure Of Isoprenoid Biosynthesis Protein With Amidotransferase-Like Domain From Ehrlichia Chaffeensis At 1. 90A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ES1 FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 46008
    Expression System Vector Type: PLASMID
    Gene: ECH_0012
    Organism Scientific: EHRLICHIA CHAFFEENSIS
    Organism Taxid: 205920
    Strain: ARKANSAS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3L3B)

(-) Sites  (0, 0)

(no "Site" information available for 3L3B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L3B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L3B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L3B)

(-) Exons   (0, 0)

(no "Exon" information available for 3L3B)

(-) 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:210
 aligned with Q2GI86_EHRCR | Q2GI86 from UniProtKB/TrEMBL  Length:221

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q2GI86_EHRCR     3 LNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESVGEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFDEDKENDYILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKDIAKVKVTIGEDSNGLIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYL 218
               SCOP domains d3l3ba_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..........hhhhhhhhhhhhhhh..eeeeee.......eee....eee....hhhhhhhhhh...eee.hhhhhhhh.eeee..hhhhhhhhh......--....hhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.....ee....----hhhhhh.ee........eee....eeeehhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l3b A   3 LNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESVGEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFDED--NDYILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKDIAKVKVTIGE----LIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYL 218
                                    12        22        32        42        52        62        72        82        92       102      |112       122       132       142       152      |  - |     172       182       192       202       212      
                                                                                                                                    109  |                                            159  164                                                      
                                                                                                                                       112                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q2GI86_EHRCR | Q2GI86 from UniProtKB/TrEMBL  Length:221

    Alignment length:218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
         Q2GI86_EHRCR     2 ALNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESVGEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFDEDKENDYILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKDIAKVKVTIGEDSNGLIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYLK 219
               SCOP domains d3l3bb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------DJ-1_PfpI-3l3bB01 B:41-195                                                                                                                                 ------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------DJ-1_PfpI-3l3bB02 B:41-195                                                                                                                                 ------------------------ Pfam domains (2)
         Sec.struct. author .eeeeee..........hhhhhhhhhhhhhhh.eeeeeee.......eee....eee....hhhhhhhhhh...eee.hhhhhhhh.eeee..hhhhhhhhh....-----...hhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.....ee.......hhhhhhh.ee........eee....eeeehhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l3b B   2 ALNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESVGEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFD-----DYILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKDIAKVKVTIGEDSNGLIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYLK 219
                                    11        21        31        41        51        61        71        81        91       101     |   - |     121       131       141       151       161       171       181       191       201       211        
                                                                                                                                   107   113
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L3B)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Glutaminase_I (73)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2GI86_EHRCR | Q2GI86)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

 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
(no "Ligands, Modified Residues, Ions" information available for 3l3b)
 
  Sites
(no "Sites" information available for 3l3b)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3l3b)
 

(-) 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 ](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
  3l3b
    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
  Q2GI86_EHRCR | Q2GI86
    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
  Q2GI86_EHRCR | Q2GI86
    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 3L3B)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3L3B)