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(-) Description

Authors :  G. Jogl, L. Tong
Date :  19 Dec 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Amp Forming; Related To Firefly Luciferase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  G. Jogl, L. Tong
Crystal Structure Of Yeast Acetyl-Coenzyme A Synthetase In Complex With Amp
Biochemistry V. 43 1425 2004
PubMed-ID: 14769018  |  Reference-DOI: 10.1021/BI035911A
(for further references see the PDB file header)

(-) Compounds

    EC Number6.2.1.1
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21 STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism Taxid4932

 Structural Features

(-) Chains, Units

Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
1AC1SOFTWAREILE A:366 , GLY A:443 , GLU A:444 , PRO A:445 , ASP A:467 , THR A:468 , TYR A:469 , TRP A:470 , GLN A:471 , THR A:472 , ASP A:559 , ILE A:571 , ARG A:574BINDING SITE FOR RESIDUE AMP A 720

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RY2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
1Tyr A:392 -Pro A:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RY2)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
1AMP_BINDINGPS00455 Putative AMP-binding domain signature.ACS1_YEAST317-328  1A:317-328
Biological Unit 1 (1, 3)
1AMP_BINDINGPS00455 Putative AMP-binding domain signature.ACS1_YEAST317-328  3A:317-328

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YAL054C1YAL054C.1I:45023-428822142ACS1_YEAST1-7137131A:74-713 (gaps)640

(-) 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:615
 aligned with ACS1_YEAST | Q01574 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:640
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713
               SCOP domains d1ry2a_ A: Acetyl-CoA synthetase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1ry2A02 A:577-713  [code=3.30.300.30, no name def            ined]                                                                        CATH domains
               Pfam domains DUF3448-1ry2A02 A:74-158                                                             ------AMP-binding-1ry2A01 A:165-606                                                                                                                                                                                                                                                                                                                                                                                                                             -------------------            ------------------DUF4009-1ry2A03 A:656-700                    ------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:74-713 (gaps) UniProt: 1-713 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623 |       -    |  643       653       663       673       683  |      -      |703       713
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 625          638                                             686           700             

   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

(-) CATH Domains  (1, 1)

Asymmetric Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
Clan: ANL (32)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (ACS1_YEAST | Q01574)
molecular function
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003987    acetate-CoA ligase activity    Catalysis of the reaction: ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA.
    GO:0016880    acid-ammonia (or amide) ligase activity    Catalysis of the ligation of an acid to ammonia (NH3) or an amide via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0019654    acetate fermentation    The anaerobic chemical reactions and pathways resulting in the breakdown of acetate, yielding energy in the form of ATP.
    GO:0006085    acetyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
    GO:0019427    acetyl-CoA biosynthetic process from acetate    The chemical reactions and pathways resulting in the formation of acetyl-CoA from acetate, either directly or via acetylphosphate.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.


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 Related Entries

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

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(-) Related Entries Specified in the PDB File