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 A HAD-SUPERFAMILY HYDROLASE FROM EHRLICHIA CHAFFEENSIS AT 1.9A RESOLUTION
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  08 Dec 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Ehrlichia Chaffeensis, Had-Superfamily Hydrolase, Hydrolase, Als Collaborative Crystallography, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, T. E. Edwards, B. Sankaran, B. Staker
Crystal Structure Of A Had-Superfamily Hydrolase From Ehrlichia Chaffeensis At 1. 9A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HAD-SUPERFAMILY HYDROLASE, SUBFAMILY IA, VARIANT 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECH_0332
    Organism Scientific: EHRLICHIA CHAFFEENSIS
    Organism Taxid: 205920
    Strain: ARKANSAS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:117 , ASN A:120 , LEU A:121 , THR A:122 , HIS A:123 , HOH A:347BINDING SITE FOR RESIDUE SO4 A 211

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:37 -Asn A:38
2Lys A:138 -Pro A:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KZX)

(-) 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:205
 aligned with Q2GHD1_EHRCR | Q2GHD1 from UniProtKB/TrEMBL  Length:210

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
         Q2GHD1_EHRCR     - -MKQPTAVIFDWYNTLIDTSINIDRTTFYQVLDQMGYKNIDLDSIPNSTIPKYLITLLGKRWKEATILYENSLEKSQKSDNFMLNDGAIELLDTLKENNITMAIVSNKNGERLRSEIHHKNLTHYFDSIIGSGDTGTIKPSPEPVLAALTNINIEPSKEVFFIGDSISDIQSAIEAGCLPIKYGSTNIIKDILSFKNFYDIRNFICQLIN 209
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------HAD_2-3kzxA01 A:7-180                                                                                                                                                         ----------------------------- Pfam domains
         Sec.struct. author ......eeee......ee.....hhhhhhhhhhhh.............hhhhhhhhhhh.hhhhhhhhhhhhhhhh......ee..hhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhhh......eeeee.hhhhhhhhhhh..eeeee..-----..eee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kzx A   0 SMKQPTAVIFDWYNTLIDTSINIDRTTFYQVLDQMGYKNIDLDSIPNSTIPKYLITLLGKRWKEATILYENSLEKSQKSDNFMLNDGAIELLDTLKENNITMAIVSNKNGERLRSEIHHKNLTHYFDSIIGSGDTGTIKPSPEPVLAALTNINIEPSKEVFFIGDSISDIQSAIEAGCLPIKYGS-----DILSFKNFYDIRNFICQLIN 209
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    |    -|      199       209
                                                                                                                                                                                                                  184   190
   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 3KZX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2GHD1_EHRCR | Q2GHD1)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:138 - Pro A:139   [ RasMol ]  
    Lys A:37 - Asn A:38   [ 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
  3kzx
    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
  Q2GHD1_EHRCR | Q2GHD1
    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
  Q2GHD1_EHRCR | Q2GHD1
    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 3KZX)

(-) Related Entries Specified in the PDB File

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