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

(-) Description

Title :  CRYSTAL STRUCTURE OF ACETATE KINASE FROM ENTAMOEBA HISTOLYTICA
 
Authors :  T. M. Thaker, M. Tanabe, T. M. Iverson
Date :  09 Sep 12  (Deposition) - 05 Dec 12  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Pyrophosphate-Dependent Acetate Kinase, Askha (Acetate And Sugar Kinase, Hsc70, Actin) Superfamily, Ribonuclease H-Like Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Thaker, M. Tanabe, M. L. Fowler, A. M. Preininger, C. Ingram-Smith, K. S. Smith, T. M. Iverson
Crystal Structures Of Acetate Kinases From The Eukaryotic Pathogens Entamoeba Histolytica And Cryptococcus Neoformans
J. Struct. Biol. V. 181 185 2013
PubMed-ID: 23159802  |  Reference-DOI: 10.1016/J.JSB.2012.11.001

(-) Compounds

Molecule 1 - ACETATE KINASE
    Chains: A, B
    EC Number: 2.7.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: YBS121
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ACKA, EHI_170010
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4H0O)

(-) Sites  (0, 0)

(no "Site" information available for 4H0O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H0O)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:160 -Pro A:161
2Arg A:283 -Gly A:284
3Gln B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H0O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H0O)

(-) Exons   (0, 0)

(no "Exon" information available for 4H0O)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4h0oa1 A:2-188 automated matches                                                                                                                                                  d4h0oa2 A:189-392 automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee..eeeeeeee...eeeeee..eeeeee....hhhhhhhhhhhhhhhh.....eeeeee..........ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhh....hhhh.eeeeeee....eeeeeee..eeeee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.....ee........eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0o A   2 SNVLIFNVGSSSLTYKVFCSDNIVCSGKSNKPFIEHHLNGQIIKIETPILNHPQAAKLIIQFLKENHISIAFVGHRFVHGGSYFKKSAVIDEVVLKELKECLPLAPIHNPSSFGVIEISMKELPTTRQYVAIDTAFHSTISQAERTYAIPQPYQSQYLKFGFHGLSYEYVINSLKNVIDVSHSKIIACHLGTGGSSCCGIVNGKSFDTSMGNSTLAGLVMSTRCGDIDPTIPIDMIQQVGIEKVVDILNKKSGLLGVSELSSDMRDILHEIETRGPKAKTCQLAFDVYIKQLAKTIGGLMVEIGGLDLLVFTDQMGLEVWQVRKAICDKMKFLGIELDDSLNEKSMGKKIEFLTMPSSKVQVCVAPNDEELVILQKGKELFQF 392
                                    11        21        31|       49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389   
                                                        31|                                                                                                                                                                                                                                                                                                                                                                
                                                         40                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4h0ob1 B:2-188 automated matches                                                                                                                                                          d4h0ob2 B:189-392 automated matches                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee....eeeeeeeee.........eeeeee..eeeeee....hhhhhhhhhhhhhhhh.....eeeeee..........ee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhh...hhhh.eeeeeee....eeeeeee..eeeee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.....ee........eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0o B   2 SNVLIFNVGSSSLTYKVFCSDNIVCSGKSNRVNVTGTEKPFIEHHLNGQIIKIETPILNHPQAAKLIIQFLKENHISIAFVGHRFVHGGSYFKKSAVIDEVVLKELKECLPLAPIHNPSSFGVIEISMKELPTTRQYVAIDTAFHSTISQAERTYAIPQPYQSQYLKFGFHGLSYEYVINSLKNVIDVSHSKIIACHLGTGGSSCCGIVNGKSFDTSMGNSTLAGLVMSTRCGDIDPTIPIDMIQQVGIEKVVDILNKKSGLLGVSELSSDMRDILHEIETRGPKAKTCQLAFDVYIKQLAKTIGGLMVEIGGLDLLVFTDQMGLEVWQVRKAICDKMKFLGIELDDSLNEKSMGKKIEFLTMPSSKVQVCVAPNDEELVILQKGKELFQF 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       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
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H0O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H0O)

(-) Gene Ontology  (13, 13)

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
(no "Ligands, Modified Residues, Ions" information available for 4h0o)
 
  Sites
(no "Sites" information available for 4h0o)
 
  Cis Peptide Bonds
    Arg A:283 - Gly A:284   [ RasMol ]  
    Gln A:160 - Pro A:161   [ RasMol ]  
    Gln B:160 - Pro B:161   [ 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 | Biol. Unit 1 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
  4h0o
    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
  C4M1C3_ENTHI | C4M1C3
    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)
  2.7.2.12
    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
  C4M1C3_ENTHI | C4M1C3
    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 4H0O)

(-) Related Entries Specified in the PDB File

4h0p