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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF A RABBIT MUSCLE FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE A DIMER VARIANT
 
Authors :  M. Sherawat, D. R. Tolan, K. N. Allen
Date :  04 Jan 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lyase, Acetylation, Glycolysis, Phosphoprotein, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sherawat, D. R. Tolan, K. N. Allen
Structure Of A Rabbit Muscle Fructose-1, 6-Bisphosphate Aldolase A Dimer Variant.
Acta Crystallogr. , Sect. D V. 64 543 2008
PubMed-ID: 18453690  |  Reference-DOI: 10.1107/S0907444908004976
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE A
    Chains: A
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPB1
    Expression System Strain: JM83
    Expression System Vector Type: PLASMID
    Gene: ALDOA
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Synonym: MUSCLE-TYPE ALDOLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
113P2Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2SO412Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:41 , ARG A:42 , ARG A:303 , HOH A:3671BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWARETHR A:51 , GLU A:52BINDING SITE FOR RESIDUE SO4 A 2
3AC3SOFTWARELYS A:12 , LYS A:199 , GLN A:202 , ARG A:258BINDING SITE FOR RESIDUE SO4 A 3
4AC4SOFTWAREHIS A:80 , LYS A:110 , HOH A:3457BINDING SITE FOR RESIDUE SO4 A 345
5AC5SOFTWARESER A:275 , HOH A:3458 , HOH A:3696BINDING SITE FOR RESIDUE SO4 A 346
6AC6SOFTWAREASP A:66 , ASP A:67 , LYS A:311 , HOH A:3451 , HOH A:3598BINDING SITE FOR RESIDUE SO4 A 347
7AC7SOFTWARELYS A:229 , LEU A:270 , SER A:271 , GLY A:272 , SER A:300 , TYR A:301 , GLY A:302 , ARG A:303 , HOH A:3655 , HOH A:3657 , HOH A:3659 , HOH A:3661 , HOH A:3667BINDING SITE FOR RESIDUE 13P A 3371

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BV4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BV4)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_CLASS_IPS00158 Fructose-bisphosphate aldolase class-I active site.ALDOA_RABIT222-232  1A:221-231
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_CLASS_IPS00158 Fructose-bisphosphate aldolase class-I active site.ALDOA_RABIT222-232  2A:221-231

(-) Exons   (0, 0)

(no "Exon" information available for 3BV4)

(-) 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:341
 aligned with ALDOA_RABIT | P00883 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:341
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344 
          ALDOA_RABIT     5 HPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTP 345
               SCOP domains d3bv4a_ A: Fructose-1,6-bisphosphate aldolase                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3bv4A00 A:4-344 Aldolase class I                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhh..eeeeeehhhhhh.......hhhhhhhh...eeeee....eee.......eee....hhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhee...............hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CL----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bv4 A   4 HPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLVGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTS 344
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BV4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALDOA_RABIT | P00883)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004332    fructose-bisphosphate aldolase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    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
    13P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:157 - Pro A:158   [ 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
  3bv4
    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
  ALDOA_RABIT | P00883
    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)
  4.1.2.13
    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
  ALDOA_RABIT | P00883
    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
        ALDOA_RABIT | P00883: 1ado 1ewd 1ewe 1ex5 1j4e 1zah 1zai 1zaj 1zal 2ot0 2ot1 2qut 2quu 2quv 3b8d 3dfn 3dfo 3dfp 3dfq 3dfs 3dft 3lge 3tu9 5f4x 5vy5 6ald

(-) Related Entries Specified in the PDB File

1ado