Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARCHAEAL ASPARAGINE SYNTHETASE A COMPLEXED WITH L-ASPARAGINE
 
Authors :  M. Blaise, D. Kern
Date :  15 Oct 10  (Deposition) - 17 Aug 11  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Asn Synthetase Bound To Asn, Seven Stranded Anti Parallel Beta Sheet, Synthetase, Asp, Asn, Amp, Ammonia, Lygase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Blaise, M. Frechin, V. Olieric, C. Charron, C. Sauter, B. Lorber, H. Roy, D. Kern
Crystal Structure Of The Archaeal Asparagine Synthetase: Interrelation With Aspartyl-Trna And Asparaginyl-Trna Synthetases.
J. Mol. Biol. V. 412 437 2011
PubMed-ID: 21820443  |  Reference-DOI: 10.1016/J.JMB.2011.07.050

(-) Compounds

Molecule 1 - ASNS-LIKE ASPARAGINYL-TRNA SYNTHETASE RELATED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ASNS-LIKE, PYRAB02460, PAB2356
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: ARCHAEAL ASPARAGINE SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ASN2Mod. Amino AcidASPARAGINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:75 , LYS A:80 , ARG A:99 , GLN A:116 , ASP A:118 , SER A:218 , GLY A:219 , ARG A:222 , ALA A:261 , GLY A:262 , HOH A:308 , HOH A:337 , HOH A:404BINDING SITE FOR RESIDUE ASN A 295
2AC2SOFTWARELYS B:80 , ARG B:99 , GLN B:116 , ASP B:118 , TYR B:194 , SER B:218 , GLY B:219 , ARG B:222 , ALA B:261 , GLY B:262 , HOH B:321 , HOH B:341 , HOH B:376 , HOH B:451BINDING SITE FOR RESIDUE ASN B 295

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P8Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:50 -Pro A:51
2Trp B:50 -Pro B:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3P8Y)

(-) Sequences/Alignments

Asymmetric/Biological 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:295
 aligned with Q9V228_PYRAB | Q9V228 from UniProtKB/TrEMBL  Length:294

    Alignment length:295
                                                                                                                                                                                                                                                                                                                               294 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   | 
         Q9V228_PYRAB     1 MNAVEIISRDIYKAIDIQTKILDYMTKFFTDRGFKWLLPIMLSPITDPLWPDPAGEGIRPAEVDVYGVRMRLTHSMILHKQLAIAMGLEKIFVLSPNIRLESRRKDDGRHSYEFTQLDFEIEGAKMKDVMRLIEELIYGLFRKAEEWTGREFPRARHFKVYDYKDILEEFGSDEKASMEMEEPFWIVNIPREFYDREENGVWKNYDLILPYGYGEVSSGGEREWEYEKIVAKIRAAGLKEDSFRPYLEIARAGKLKPSAGAGIGVERLVRFIVGAKHIAEVQPFPRVPGIPAVI-   -
               SCOP domains d3p8ya_ A: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eee....ee..................eeee..eeeee...hhhhhhhhhhh...eeeeeeeee...hhhhh......eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..........eeehhhhhhhhhhhhhhhhhh...eeee.........ee..ee.eeeeee....eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhh..hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p8y A   1 MNAVEIISRDIYKAIDIQTKILDYMTKFFTDRGFKWLLPIMLSPITDPLWPDPAGEGIRPAEVDVYGVRMRLTHSMILHKQLAIAMGLEKIFVLSPNIRLESRRKDDGRHSYEFTQLDFEIEGAKMKDVMRLIEELIYGLFRKAEEWTGREFPRARHFKVYDYKDILEEFGSDEKASMEMEEPFWIVNIPREFYDREENGVWKNYDLILPYGYGEVSSGGEREWEYEKIVAKIRAAGLKEDSFRPYLEIARAGKLKPSAGAGIGVERLVRFIVGAKHIAEVQPFPRVPGIPAVIN 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with Q9V228_PYRAB | Q9V228 from UniProtKB/TrEMBL  Length:294

    Alignment length:295
                                                                                                                                                                                                                                                                                                                               294 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   | 
         Q9V228_PYRAB     1 MNAVEIISRDIYKAIDIQTKILDYMTKFFTDRGFKWLLPIMLSPITDPLWPDPAGEGIRPAEVDVYGVRMRLTHSMILHKQLAIAMGLEKIFVLSPNIRLESRRKDDGRHSYEFTQLDFEIEGAKMKDVMRLIEELIYGLFRKAEEWTGREFPRARHFKVYDYKDILEEFGSDEKASMEMEEPFWIVNIPREFYDREENGVWKNYDLILPYGYGEVSSGGEREWEYEKIVAKIRAAGLKEDSFRPYLEIARAGKLKPSAGAGIGVERLVRFIVGAKHIAEVQPFPRVPGIPAVI-   -
               SCOP domains d3p8yb_ B: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eee....ee..................eeee..eeeee...hhhhhhhhhhh...eeeeeeeee...hhhhh......eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..........eeehhhhhhhh.hhhhhhhhh...eeee.........ee..ee.eeeeee....eeeeeeee...hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhh..hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p8y B   1 MNAVEIISRDIYKAIDIQTKILDYMTKFFTDRGFKWLLPIMLSPITDPLWPDPAGEGIRPAEVDVYGVRMRLTHSMILHKQLAIAMGLEKIFVLSPNIRLESRRKDDGRHSYEFTQLDFEIEGAKMKDVMRLIEELIYGLFRKAEEWTGREFPRARHFKVYDYKDILEEFGSDEKASMEMEEPFWIVNIPREFYDREENGVWKNYDLILPYGYGEVSSGGEREWEYEKIVAKIRAAGLKEDSFRPYLEIARAGKLKPSAGAGIGVERLVRFIVGAKHIAEVQPFPRVPGIPAVIN 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P8Y)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9V228_PYRAB | Q9V228)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    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:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ASN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:50 - Pro A:51   [ RasMol ]  
    Trp B:50 - Pro B:51   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3p8y
    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
  Q9V228_PYRAB | Q9V228
    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)
  (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
  Q9V228_PYRAB | Q9V228
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9V228_PYRAB | Q9V228: 3p8t 3p8v 3reu 3rex 3rl6

(-) Related Entries Specified in the PDB File

3p8t 3p8v 3reu 3rex