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 LEURS EDITING DOMAIN OF CANDIDA ALBICANS MUTANT K510A IN COMPLEX WITH THE ADDUCT FORMED BY AN2690-AMP
 
Authors :  H. Zhao, A. Palencia, E. Seiradake, Z. Ghaemi, Z. Luthey-Schulten, S. C S. A. Martinis
Date :  02 Feb 15  (Deposition) - 01 Jul 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Aminoacylation, Protein Synthesis, Proof-Reading Mechanisms, Antifungal Target (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhao, A. Palencia, E. Seiradake, Z. Ghaemi, S. Cusack, Z. Luthey-Schulten, S. Martinis
Analysis Of The Resistance Mechanism Of A Benzoxaborole Inhibitor Reveals Insight Into The Leucyl-Trna Synthetase Editing Mechanism.
Acs Chem. Biol. V. 10 2277 2015
PubMed-ID: 26172575  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00291

(-) Compounds

Molecule 1 - POTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE
    Atcc: MYA-2876
    Chains: A
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Expression System Variant: DH10B
    Expression System Vector: PET21D
    Expression System Vector Type: PLASMID
    Fragment: EDITING DOMAIN (CP1), UNP RESIDUES 280-530
    Mutation: YES
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 237561
    Strain: SC5314

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ANZ1Ligand/Ion[(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYLDIHYDROGEN PHOSPHATE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:315 , THR A:316 , LEU A:317 , ARG A:318 , THR A:321 , ARG A:366 , VAL A:403 , LEU A:404 , LYS A:407 , VAL A:412 , ASP A:418 , SER A:419 , LYS A:483 , GOL A:1532 , HOH A:2024 , HOH A:2125 , HOH A:2126 , HOH A:2128 , HOH A:2133 , HOH A:2138 , HOH A:2249BINDING SITE FOR RESIDUE ANZ A 600
2AC2SOFTWARELEU A:317 , ARG A:318 , ARG A:366 , LYS A:483 , TYR A:487 , ANZ A:600 , HOH A:2207BINDING SITE FOR RESIDUE GOL A1532
3AC3SOFTWAREARG A:286 , LYS A:309 , TYR A:311 , TYR A:501 , ASP A:504 , HOH A:2097BINDING SITE FOR RESIDUE GOL A1533

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AGI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AGI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AGI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AGI)

(-) Exons   (0, 0)

(no "Exon" information available for 5AGI)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhh.......eeeeeeee.hhhhhhhh.eeee....eeeeeeee..eeeeehhhhhhhhhh.............eeeehhhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhh......hhhhh.......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5agi A 279 GYVGIKIRLTDVAPQAQELFKKESLDVKENKVYLVAATLRPETMYGQTCCFVSPKIDYGVFDAGNGDYFITTERAFKNMSFQNLTPKRGYYKPLFTINGKTLIGSRIDAPYAVNKNLRVLPMETVLATKGTGVVTCVPSDSPDDFVTTRDLANKPEYYGIEKDWVQTDIVPIVHTEKYGDKCAEFLVNDLKIQSPKDSVQLANAKELAYKEGFYNGTMLIGKYKGDKVEDAAPKVKQDLIDEGLAFVYNEPE 530
                                   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528
   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 5AGI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AGI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AGI)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    ANZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5agi)
 

(-) 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
  5agi
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  6.1.1.4
    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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 5AGI)

(-) Related Entries Specified in the PDB File

5agh CRYSTAL STRUCTURE OF THE LEURS EDITING DOMAIN OF CANDIDA ALBICANS MUTANT K510A
5agj CRYSTAL STRUCTURE OF THE LEURS EDITING DOMAIN OF CANDIDA ALBICANS IN COMPLEX WITH THE ADDUCT AN2690-AMP
5ah5 CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AGROBACTERIUM RADIOBACTER K84 AGNB2 LEURS-TRNA-LEUAMS