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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P1)
 
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 :  18 Nov 15  (Deposition) - 22 Jun 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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 SYNTHASE
    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 272-687
    Gene: PFF1095W
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Other Details: DELETION OF RESIDUES 475-519, C273S SUBSTITUTION TO PREVENT DISULFIDE BONDS, GAM INSERTED AT N- TERM (EXPRESSION VECTOR)
    Strain: ISOLATE 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FO4)

(-) Sites  (0, 0)

(no "Site" information available for 5FO4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FO4)

(-) 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 5FO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FO4)

(-) Exons   (0, 0)

(no "Exon" information available for 5FO4)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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 ..eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee..........eehhhhhhhhh.eeeeehhhhhhhhhhh....ee....eeeeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fo4 A 273 SQEYTLIKIFVSNVKDFYSIFMNSIRSSQSVLNTFFTDFEKGEEDLKNKIWNEDFFVKDKKVIFLGSTLKPETAYGQNYTFINPNEYYYLTLGFDKQNLHVNNIMTKEEIINSCPNIYVCSENSLYNLAYQGIIPLLKDVFILNKIKGEHFVGLETYTNISKIKNLYILPMTTIKMNISTGIVPCVSSDSTDDYACLEDIRKKKNYYCEKYNLKEEQLKNNSESCIELPEIGNNTGKYYYEKEKVSSYKDVKLQKIKEVLYKKQYFEGIMTVDPYKGMKTFNCRKLAKQNIIRNLDGFLYSE 687
                                   282       292       302  ||   367       377       387       397       407       417       427|      443       453       463       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685  
                                                          305|                                                               427|                                  471|                                                                                                                                                                   
                                                           361                                                                434                                   524                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee...hhhhhh.......eehhhhhhhhh.eeeee..hhhhhhhhh....ee.............eeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......ee......hhhhhhhhhh........hhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fo4 B 273 SQEYTLIKIFVSNVKDFYSIFMNSIRSSQSVLNACTFFTDFEKGEEDLKNKIWNEDFFVKDKKVIFLGSTLKPETAYGQNYTFINPNEYYYLTLGFDKQNLHYGDKSYVNNIMTKEEIINSCPNIYVCSENSLYNLAYQGIIPLLKNKNGNLDDVFILNKIKGEHFVGLETYTNISKIKNLYILPMTTIKMNISTGIVPCVSSDSTDDYACLEDIRKKKNYYCEKYNLKEEQLKNNSESCIELPEIGNNTGKYYYEKEKVSSYKDVKLQKIKEVLYKKQYFEGIMTVDPYKGMKTFNCRKLAKQNIIRNLDGFLYSE 687
                                   282       292       302    || 365       375       385       395       405       415       425       435       445       455       465       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       
                                                            307|                                                                                                              474|                                                                                                                                                                       
                                                             361                                                                                                               520
   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 5FO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FO4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FO4)

(-) Gene Ontology  (12, 12)

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  Cis Peptide Bonds
    Asp A:658 - Pro A:659   [ RasMol ]  
    Asp B:658 - Pro B:659   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        C6KT64_PLAF7 | C6KT64: 5foc 5fod

(-) Related Entries Specified in the PDB File

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
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)