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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  FULL LENGTH STRUCTURE OF CYSTATHIONINE BETA-SYNTHASE FROM DROSOPHILA IN COMPLEX WITH AMINOACRYLATE
 
Authors :  M. Koutmos, J. L. Smith
Date :  21 Oct 10  (Deposition) - 01 Dec 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Cbs, Synthase, Plp, Heme, Aminoacrylate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Koutmos, O. Kabil, J. L. Smith, R. Banerjee
Structural Basis For Substrate Activation And Regulation By Cystathionine Beta-Synthase (Cbs) Domains In Cystathionine {Beta}-Synthase.
Proc. Natl. Acad. Sci. Usa V. 107 20958 2010
PubMed-ID: 21081698  |  Reference-DOI: 10.1073/PNAS.1011448107

(-) Compounds

Molecule 1 - CG1753, ISOFORM A
    Chains: A
    EC Number: 4.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CG1753, DMEL_CG1753
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: CG1753, ISOFORM B, LD21426P

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2P1T1Ligand/Ion2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2P1T1Ligand/Ion2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2P1T2Ligand/Ion2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:20 , LYS A:21 , CYS A:22 , LYS A:23 , TRP A:24 , THR A:28 , GLU A:30 , SER A:32 , PRO A:33 , HIS A:34 , ARG A:193 , ALA A:195 , PRO A:198 , TYR A:202 , ARG A:235 , HOH A:615 , HOH A:628 , HOH A:644 , HOH A:868 , HOH A:924 , HOH A:1017BINDING SITE FOR RESIDUE HEM A 701
2AC2SOFTWARELYS A:88 , THR A:115 , SER A:116 , GLY A:117 , ASN A:118 , THR A:119 , GLN A:191 , ALA A:224 , GLY A:225 , THR A:226 , ALA A:227 , GLY A:228 , THR A:229 , GLY A:274 , ILE A:275 , SER A:318 , PRO A:344 , ASP A:345 , HOH A:726 , HOH A:771 , HOH A:798 , HOH A:930BINDING SITE FOR RESIDUE P1T A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PC3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:258 -Pro A:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PC3)

(-) Exons   (0, 0)

(no "Exon" information available for 3PC3)

(-) 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:504
 aligned with Q9VRD9_DROME | Q9VRD9 from UniProtKB/TrEMBL  Length:522

    Alignment length:504
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506    
         Q9VRD9_DROME     7 YERPADFIDPGKPSKCKWHLGTAEKSPHIHRGIAHRQQITPNILEVIGCTPLVKLNNIPASDGIECEMYAKCEFLNPGGSVKDRIGYRMVQDAEEQGLLKPGYTIIEPTSGNTGIGLAMACAVKGYKCIIVMPEKMSNEKVSALRTLGAKIIRTPTEAAYDSPEGLIYVAQQLQRETPNSIVLDQYRNAGNPLAHYDGTAAEILWQLDNKVDMIVVSAGTAGTISGIGRKIKEQVPSCQIVGVDPYGSILARPAELNKTDVQFYEVEGIGYDFPPTVFDDTVVDVWTKIGDSDCFPMSRRLNAEEGLLCGGSSGGAMHAALEHARKLKKGQRCVVILPDGIRNYMTKFVSDNWMEARNFKEPVNEHGHWWWSLAIAELELPAPPVILKSDATVGEAIALMKKHRVDQLPVVDQDDGSVLGVVGQETLITQIVSMNRQQSDPAIKALNKRVIRLNESEILGKLARVLEVDPSVLILGKNPAGKVELKALATKLDVTTFIAAGKQK 510
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------PALP-3pc3A02 A:49-345                                                                                                                                                                                                                                                                                    -----------------------------------CBS-3pc3A01 A:381-439                                      ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................hhhhhh....eee..hhhhhh....eeeeee.hhh.....hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee..........hhhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......eeeeee..hhhhhh....hhhhhhhh................hhhhhh.......ee...hhhhhhhhhhhhh..eeeee......eeeeeehhhhhhhhhhhh.....hhhh.ee....eee...hhhhhhhhhh...eeeeeee.....eeeeeeeehhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pc3 A   7 YERPADFIDPGKPSKCKWHLGTAEKSPHIHRGIAHRQQITPNILEVIGCTPLVKLNNIPASDGIECEMYAKCEFLNPGGSVKDRIGYRMVQDAEEQGLLKPGYTIIEPTSGNTGIGLAMACAVKGYKCIIVMPEKMSNEKVSALRTLGAKIIRTPTEAAYDSPEGLIYVAQQLQRETPNSIVLDQYRNAGNPLAHYDGTAAEILWQLDNKVDMIVVSAGTAGTISGIGRKIKEQVPSCQIVGVDPYGSILARPAELNKTDVQFYEVEGIGYDFPPTVFDDTVVDVWTKIGDSDCFPMSRRLNAEEGLLCGGSSGGAMHAALEHARKLKKGQRCVVILPDGIRNYMTKFVSDNWMEARNFKEPVNEHGHWWWSLAIAELELPAPPVILKSDATVGEAIALMKKHRVDQLPVVDQDDGSVLGVVGQETLITQIVSMNRQQSDPAIKALNKRVIRLNESEILGKLARVLEVDPSVLILGKNPAGKVELKALATKLDVTTFIAAGKQK 510
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506
   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 3PC3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PC3)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: CBS] (51)
(-)
Clan: no clan defined [family: PALP] (67)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9VRD9_DROME | Q9VRD9)
molecular function
    GO:0004122    cystathionine beta-synthase activity    Catalysis of the reaction: L-serine + L-homocysteine = cystathionine + H2O.
    GO:0004124    cysteine synthase activity    Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019344    cysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0006535    cysteine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.
    GO:0019343    cysteine biosynthetic process via cystathionine    The chemical reactions and pathways resulting in the formation of cysteine, via the intermediate cystathionine.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P1T  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:258 - Pro A:259   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3pc3
    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
  Q9VRD9_DROME | Q9VRD9
    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)
  4.2.1.22
    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
  Q9VRD9_DROME | Q9VRD9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9VRD9_DROME | Q9VRD9: 3pc2 3pc4

(-) Related Entries Specified in the PDB File

3pc2 3pc4