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(-) Description

Title :  X-RAY STRUCTURE OF ADENOSINE 5'-MONOPHOSPHATE DEAMINASE FROM ARABIDOPSIS THALIANA IN COMPLEX WITH COFORMYCIN 5'-PHOSPHATE
 
Authors :  B. W. Han, G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Ces
Date :  25 Jun 05  (Deposition) - 19 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.34
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Atampd, At2G38280, Adenosine 5'-Monophosphate Deaminase, Coformycin 5'-Phosphate, Structural Genomics, Protein Structure Initiative, Psi, Cesg, Center For Eukaryotic Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. W. Han, C. A. Bingman, D. K. Mahnke, R. M. Bannen, S. Y. Bednarek, R. L. Sabina, G. N. Phillips
Membrane Association, Mechanism Of Action, And Structure Of Arabidopsis Embryonic Factor 1 (Fac1).
J. Biol. Chem. V. 281 14939 2006
PubMed-ID: 16543243  |  Reference-DOI: 10.1074/JBC.M513009200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMP DEAMINASE
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidP2BAC
    Expression System Taxid7108
    Expression System VectorBACULOVIRUS
    Expression System Vector TypeVIRUS
    GeneAT2G38280
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymAMPD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A
Biological Unit 2 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CF51Ligand/IonCOFORMYCIN 5'-PHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CF52Ligand/IonCOFORMYCIN 5'-PHOSPHATE
2PO42Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CF54Ligand/IonCOFORMYCIN 5'-PHOSPHATE
2PO44Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:391 , HIS A:393 , HIS A:659 , ASP A:736 , CF5 A:841BINDING SITE FOR RESIDUE ZN A 840
2AC2SOFTWAREARG A:380 , ARG A:386BINDING SITE FOR RESIDUE PO4 A 842
3AC3SOFTWAREILE A:220 , HIS A:391 , HIS A:393 , LYS A:462 , PHE A:463 , LYS A:466 , TYR A:467 , HIS A:659 , GLU A:662 , HIS A:681 , SER A:708 , ASP A:736 , ASP A:737 , GLN A:740 , ZN A:840BINDING SITE FOR RESIDUE CF5 A 841

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A3L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A3L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A3L)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1A_DEAMINASEPS00485 Adenosine and AMP deaminase signature.AMPD_ARATH732-738  1A:732-738
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1A_DEAMINASEPS00485 Adenosine and AMP deaminase signature.AMPD_ARATH732-738  2A:732-738
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1A_DEAMINASEPS00485 Adenosine and AMP deaminase signature.AMPD_ARATH732-738  4A:732-738

(-) Exons   (0, 0)

(no "Exon" information available for 2A3L)

(-) 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:616
 aligned with AMPD_ARATH | O80452 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:628
                                   221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831        
           AMPD_ARATH   212 QPDPIAADILRKEPEQETFVRLNVPLEVPTSDEVEAYKCLQECLELRKRYVFQETVAPWEKEVISDPSTPKPNTEPFAHYPQGKSDHCFEMQDGVVHVFANKDAKEDLFPVADATAFFTDLHHVLKVIAAGNIRTLCHRRLVLLEQKFNLHLMLNADKEFLAQKSAPHRDFYNVRKVDTHVHHSACMNQKHLLRFIKSKLRKEPDEVVIFRDGTYLTLREVFESLDLTGYDLNVDLLDVHADKSTFHRFDKFNLKYNPCGQSRLREIFLKQDNLIQGRFLGEITKQVFSDLEASKYQMAEYRISIYGRKMSEWDQLASWIVNNDLYSENVVWLIQLPRLYNIYKDMGIVTSFQNILDNIFIPLFEATVDPDSHPQLHVFLKQVVGFDLVDDESKPERRPTKHMPTPAQWTNAFNPAFSYYVYYCYANLYVLNKLRESKGMTTITLRPHSGEAGDIDHLAATFLTCHSIAHGINLRKSPVLQYLYYLAQIGLAMSPLSNNSLFLDYHRNPFPVFFLRGLNVSLSTDDPLQIHLTKEPLVEEYSIAASVWKLSACDLCEIARNSVYQSGFSHALKSHWIGKDYYKRGPDGNDIHKTNVPHIRVEFRDTIWKEEMQQVYLGKAVISDEVVP 839
               SCOP domains d2a3la1 A:212-839 AMP deaminase (AMPD), catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................hhhhhhhhhhhhhh.............------------......................................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.....hhhhhhhhhhhhhhh......eee..eeehhhhhhhhhh.........................hhhhhh....hhhhhhhh.........hhhhhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhh.......eeeeeeee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeee..........................hhhhhhhhhhhhhhhhhhhhh.......ee.........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..eeehhhhhh.........hhhhhhhh...eee...hhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A_DEAMI----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3l A 212 QPDPIAADILRKEPEQETFVRLNVPLEVPTSDEVEAYKCLQECLELRKRYVFQETVAPWEKE------------EPFAHYPQGKSDHCFEMQDGVVHVFANKDAKEDLFPVADATAFFTDLHHVLKVIAAGNIRTLCHRRLVLLEQKFNLHLMLNADKEFLAQKSAPHRDFYNVRKVDTHVHHSACMNQKHLLRFIKSKLRKEPDEVVIFRDGTYLTLREVFESLDLTGYDLNVDLLDVHADKSTFHRFDKFNLKYNPCGQSRLREIFLKQDNLIQGRFLGEITKQVFSDLEASKYQMAEYRISIYGRKMSEWDQLASWIVNNDLYSENVVWLIQLPRLYNIYKDMGIVTSFQNILDNIFIPLFEATVDPDSHPQLHVFLKQVVGFDLVDDESKPERRPTKHMPTPAQWTNAFNPAFSYYVYYCYANLYVLNKLRESKGMTTITLRPHSGEAGDIDHLAATFLTCHSIAHGINLRKSPVLQYLYYLAQIGLAMSPLSNNSLFLDYHRNPFPVFFLRGLNVSLSTDDPLQIHLTKEPLVEEYSIAASVWKLSACDLCEIARNSVYQSGFSHALKSHWIGKDYYKRGPDGNDIHKTNVPHIRVEFRDTIWKEEMQQVYLGKAVISDEVVP 839
                                   221       231       241       251       261       271 |       -    |  291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831        
                                                                                       273          286                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         

   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  (0, 0)

(no "CATH Domain" information available for 2A3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A3L)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMPD_ARATH | O80452)
molecular function
    GO:0003876    AMP deaminase activity    Catalysis of the reaction: AMP + H2O = IMP + NH3.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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).
    GO:0043424    protein histidine kinase binding    Interacting selectively and non-covalently with protein histidine kinase.
biological process
    GO:0032264    IMP salvage    Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0009793    embryo development ending in seed dormancy    The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
    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.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0009168    purine ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0009737    response to abscisic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abscisic acid stimulus.
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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0031307    integral component of mitochondrial outer membrane    The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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