Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE P.KNOWLESI CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN
 
Authors :  A. Palencia, E. Sonoiki, D. Guo, V. Ahyong, C. Dong, X. Li, V. S. Hernande J. Legac, R. Cooper, M. R. K. Alley, Y. R. Freund, J. Derisi, S. Cusack, P. J. Rosenthal
Date :  19 Nov 15  (Deposition) - 22 Jun 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ligase, Leucine-Trna Ligase (Leurs) Activity, Atp + L-Leucine + Trna(Leucine) Gives Amp + Diphosphate + L-Leucyl-Trna(Leucine), Aminoacyl-Trna Synthetase, Protein Biosynthesis, Novel Boron Inhibitors Of Leurs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Sonoiki, A. Palencia, D. Guo, V. Ahyong, C. Dong, X. Li, V. S. Hernandez, Y. K. Zhang, W. Choi, J. Gut, J. Legac, R. Cooper, M. R. Alley, Y. R. Freund, J. Derisi, S. Cusack, P. J. Rosenthal
Anti-Malarial Benzoxaboroles Target P. Falciparum Leucyl- Trna Synthetase.
Antimicrob. Agents Chemother. V. 60 4886 2016
PubMed-ID: 27270277  |  Reference-DOI: 10.1128/AAC.00820-16

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE
    Chains: A, B, C, D
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-11
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Variant: DE3 RIL
    Fragment: EDITING DOMAIN, UNP RESIDUES 266-399,433-600
    Organism Scientific: PLASMODIUM KNOWLESI
    Organism Taxid: 5851
    Strain: H

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FOF)

(-) Sites  (0, 0)

(no "Site" information available for 5FOF)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:267 -D:267

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:538 -Pro A:539
2Glu B:538 -Pro B:539
3Glu C:538 -Pro C:539
4Glu D:538 -Pro D:539

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FOF)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.hhh.eeeeeeee.hhhhhhhhhhhhhhh...hhhhhhhheeeeeeee.hhhhhhhh.eeee....eeeeeee................eehhhhhhhhh.eeeee..hhhhhhhhh....ee...........eeeeeehhhhh..eee........eeeee............eee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fof A 258 LYFQGAMGKCQEFTLIKIYVHDYKEFYEIYLRNKKLENVNENFFSQKKIILLASTLKPETAYGQNYTFVNPGEYYYVTLGFNKQRLHYGDKNYVNNVMTRDEIIDSCENVYICSENSLYNLAYQGVIPMLSKGSSPFSDLLILMKIKGEELVGLRTYSNLSEKKDLYILPMTTIKMNIATAIVPCVSSDSADDYACLQDIRRKQAYYCEKYNLKDEFLHNESFSCIQLPDIGDNTGKYFYEMEKISSYKDAKLQKVKETLYKKQYFEGTMTVEPYKGMKIYNCRKLVKQYIIKNNEGFLYSE 567
                                   267       277       287     ||305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565  
                                                             293|                                                                                                                                                                                                                                                                         
                                                              302                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.....eeeeeeee.hhhhhhhhhhhh....hhhhhhh.eeeeeeee.hhhhhhhh.eeee....eeeeeee........hhhhhhhhh.eeeeee..hhhhhhhh.................eeeeeehhhhh..eee........eeeee............eee....hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fof B 258 LYFQGAMGKCQEFTLIKIYVHDYKEFYEIYLRNKENVNENFFSQKKIILLASTLKPETAYGQNYTFVNPGEYYYVTLGFNKQRNVMTRDEIIDSCENVYICSENSLYNLAYQGVIPMLSKGSSPFSDLLILMKIKGEELVGLRTYSNLSEKKDLYILPMTTIKMNIATAIVPCVSSDSADDYACLQDIRRKQAYYCEKYNLKDEFLHNESFSCIQLPDIGDNTGKYFYEMEKISSYKDAKLQKVKETLYKKQYFEGTMTVEPYKGMKIYNCRKLVKQYIIKNNEGFLYSE 567
                                   267       277       287   ||  307       317       327       337       347  ||   367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567
                                                           291|                                             350|                                                                                                                                                                                                              
                                                            302                                              361                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.....eeeeeeee.hhhhhhhhhhhh...hhhhhhhheeeeeeee.hhhhhhhh.eeee....eeeeeee..................hhhhhhhhh.eeeee...hhhhhhhh.................eeeeeehhhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhh.....ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fof C 258 LYFQGAMGKCQEFTLIKIYVHDYKEFYEIYLRNENVNENFFSQKKIILLASTLKPETAYGQNYTFVNPGEYYYVTLGFNKQRLHYGDKNYVNNVMTRDEIIDSCENVYICSENSLYNLAYQGVIPMLSKGSSPFSDLLILMKIKGEELVGLRTYSNLSEKKDLYILPMTTIKMNIATAIVPCVSSDSADDYACLQDIRRKQAYYCEKYNLKDEFLHNESFSCIQLPDIGDNTGKYFYEMEKISSYKDAKLQKVKETLYKKQYFEGTMTVEPYKGMKIYNCRKLVKQYIIKNNEGFLYSE 567
                                   267       277       287  ||   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558         
                                                          290|                                                                                                                                                                                                                                                                         
                                                           302                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.....eeeeeeee.hhhhhhhhhhhhhh....hhhhhhhheeeeeeee.hhhhh....eeee....eeeeeee................eehhhhhhhhh.eeeee...hhhhhhhh....ee...........eeeeeehhhhh..eeee.......eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fof D 258 LYFQGAMGKCQEFTLIKIYVHDYKEFYEIYLRNKKLENVNENFFSQKKIILLASTLKPETAYGQNYTFVNPGEYYYVTLGFNKQRLHYGDKNYVNNVMTRDEIIDSCENVYICSENSLYNLAYQGVIPMLSKGSSPFSDLLILMKIKGEELVGLRTYSNLSEKKDLYILPMTTIKMNIATAIVPCVSSDSADDYACLQDIRRKQAYYCEKYNLKDEFLHNESFSCIQLPDIGDNTGKYFYEMEKISSYKDAKLQKVKETLYKKQYFEGTMTVEPYKGMKIYNCRKLVKQYIIKNNEGFLYSE 567
                                   267       277       287     ||305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565  
                                                             293|                                                                                                                                                                                                                                                                         
                                                              302
   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 5FOF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 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
(no "Ligands, Modified Residues, Ions" information available for 5fof)
 
  Sites
(no "Sites" information available for 5fof)
 
  Cis Peptide Bonds
    Glu A:538 - Pro A:539   [ RasMol ]  
    Glu B:538 - Pro B:539   [ RasMol ]  
    Glu C:538 - Pro C:539   [ RasMol ]  
    Glu D:538 - Pro D:539   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  5fof
    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
  B3L7I1_PLAKH | B3L7I1
    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)
  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
  B3L7I1_PLAKH | B3L7I1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5fo4 CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P1)
5foc CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P21)
5fod CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P1) CONTAINING DELETIONS OF INSERTIONS 1 AND 3
5fog CRYSTAL STRUCTURE OF HTE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH A POST-TRANSFER EDITING ANALOGUE OF NORVALINE (NV2AA)
5fol CRYSTAL STRUCTURE OF THE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH A POST-TRANSFER EDITING ANALOGUE OF ISOEUCINE (ILE2AA)
5fom CRYSTAL STRUCTURE OF THE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH THE ADDUCT AMP-AN6426
5fon CRYSTAL STRUCTURE OF THE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN (APO STRUCTURE)