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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P1) CONTAINING DELETIONS OF INSERTIONS 1 AND 3
 
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 :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, P. Falciparum, 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
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PETM-11
    Expression System Taxid: 83333
    Expression System Variant: DE3 RIL
    Expression System Vector Type: PLASMID
    Fragment: EDITING DOMAIN, UNP RESIDUES 274-329,361-474,521-687
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:395 , LEU B:396 , HOH B:2081BINDING SITE FOR RESIDUE EDO B1688

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:658 -Pro A:659
2Asp B:658 -Pro B:659

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FOD)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee........eehhhhhhhhh.eeeeehhhhhhhhhhh....ee....eeeeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fod A 273 SQEYTLIKIFVSNVKDFYSIFMNSIRSSQSVLNACGTFFTDFEKGEEDLKNKIWNEDFFVKDKKVIFLGSTLKPETAYGQNYTFINPNEYYYLTLGFDKQNLHNIMTKEEIINSCPNIYVCSENSLYNLAYQGIIPLLKDVFILNKIKGEHFVGLETYTNISKIKNLYILPMTTIKMNISTGIVPCVSSDSTDDYACLEDIRKKKNYYCEKYNLKEEQLKNNSESCIELPEIGNNTGKYYYEKEKVSSYKDVKLQKIKEVLYKKQYFEGIMTVDPYKGMKTFNCRKLAKQNIIRNLDGFLYSE 687
                                   282       292       302    || 364       374       384       394       404       414       424  ||   442       452       462       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684   
                                                            307|                                                                427|                                471|                                                                                                                                                                   
                                                             360                                                                 436                                 524                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee...hhhhhh.......eehhhhhhhhh.eeeee...hhhhhhhh....ee.............eeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fod B 274 QEYTLIKIFVSNVKDFYSIFMNSIRSSQSVLNACTFFTDFEKGEEDLKNKIWNEDFFVKDKKVIFLGSTLKPETAYGQNYTFINPNEYYYLTLGFDKQNLHYGDKSYVNNIMTKEEIINSCPNIYVCSENSLYNLAYQGIIPLLKNKNGNLDDVFILNKIKGEHFVGLETYTNISKIKNLYILPMTTIKMNISTGIVPCVSSDSTDDYACLEDIRKKKNYYCEKYNLKEEQLKNNSESCIELPEIGNNTGKYYYEKEKVSSYKDVKLQKIKEVLYKKQYFEGIMTVDPYKGMKTFNCRKLAKQNIIRNLDGFLYSE 687
                                   283       293       303   ||  366       376       386       396       406       416       426       436       446       456       466      |521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681      
                                                           307|                                                                                                             473|                                                                                                                                                                        
                                                            361                                                                                                              519
   Legend:   → Mismatch (orange background)
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  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 5FOD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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 Related Entries

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

UniProtKB/TrEMBL
        C6KT64_PLAF7 | C6KT64: 5fo4 5foc

(-) 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)
5fof CRYSTAL STRUCTURE OF THE P.KNOWLESI CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN
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)