Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF AT1G77540-COENZYME A COMPLEX
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  31 May 07  (Deposition) - 19 Jun 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A  (4x)
Biol. Unit 1:  A  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Coa, Coenzyme-A, Cog2388 Family, Acetyltransferase, At1G77540, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744  |  Reference-DOI: 10.1016/J.STR.2007.06.019

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN AT1G77540
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP13-GW
    Expression System Strain: BL834(DE3) PLACI+RARE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 12-114
    Gene: AT1G77540, T5M16.13
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: CV. COLUMBIA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (4x): A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:22 , THR A:42 , TYR A:43 , VAL A:44 , ARG A:49 , GLY A:50 , LEU A:51 , GLY A:52 , LEU A:53 , ALA A:54 , SER A:77 , TYR A:78 , THR A:82 , ARG A:86 , SER A:89 , TRP A:90 , HOH A:105 , HOH A:120 , HOH A:144 , HOH A:156 , HOH A:167BINDING SITE FOR RESIDUE COA A 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q4Y)

(-) Cis Peptide Bonds  (1, 4)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4Pro A:5 -Pro A:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q4Y)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNAT_YJDJPS51729 Yjdj-type Gcn5-related N-acetyltransferase (GNAT) domain profile.Y1754_ARATH18-106  1A:7-95
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNAT_YJDJPS51729 Yjdj-type Gcn5-related N-acetyltransferase (GNAT) domain profile.Y1754_ARATH18-106  1A:7-95

(-) Exons   (0, 0)

(no "Exon" information available for 2Q4Y)

(-) 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:91
 aligned with Y1754_ARATH | Q9CAQ2 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:91
                                    25        35        45        55        65        75        85        95       105 
          Y1754_ARATH    16 PPKIVWNEGKRRFETEDHEAFIEYKMRNNGKVMDLVHTYVPSFKRGLGLASHLCVAAFEHASSHSISIIPSCSYVSDTFLPRNPSWKPLIH 106
               SCOP domains d2q4ya_ A: Hypothetical protein AT1g77540                                                   SCOP domains
               CATH domains 2q4yA00 A:5-95  [code=3.40.630.30, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeee.....eeeeeee....eeeeeeee.hhhhh..hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GNAT_YJDJ  PDB: A:7-95 UniProt: 18-106                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2q4y A   5 PPKIVWNEGKRRFETEDHEAFIEYKMRNNGKVMDLVHTYVPSFKRGLGLASHLCVAAFEHASSHSISIIPSCSYVSDTFLPRNPSWKPLIH  95
                                    14        24        34        44        54        64        74        84        94
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q4Y)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Y1754_ARATH | Q9CAQ2)
molecular function
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

 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
    COA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:5 - Pro A:6   [ 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
  2q4y
    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
  Y1754_ARATH | Q9CAQ2
    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)
  (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
  Y1754_ARATH | Q9CAQ2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Y1754_ARATH | Q9CAQ2: 1xmt 2evn 2il4 2q44

(-) Related Entries Specified in the PDB File

1xmt X-RAY STRUCTURE OF AT1G77540
2evn NMR SOLUTION STRUCTURE OF AT1G77540
2il4 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.