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(-) Description

Title :  CRYSTAL STRUCTURE OF A LIGA INHIBITOR
 
Authors :  P. A. Boriack-Sjodin, D. B. Prince
Date :  30 Jun 13  (Deposition) - 25 Dec 13  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Inhibitor Complex, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Murphy-Benenato, H. Wang, H. M. Mcguire, H. E. Davis, N. Gao, D. B. Prince, H. Jahic, S. S. Stokes, P. A. Boriack-Sjodin
Identification Through Structure-Based Methods Of A Bacterial Nad(+)-Dependent Dna Ligase Inhibitor That Avoids Known Resistance Mutations.
Bioorg. Med. Chem. Lett. V. 24 360 2014
PubMed-ID: 24287382  |  Reference-DOI: 10.1016/J.BMCL.2013.11.007

(-) Compounds

Molecule 1 - DNA LIGASE
    Chains: A
    EC Number: 6.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: ?469008
    Fragment: ADENYLATION DOMAIN, UNP RESIDUES 1-323
    Gene: EF_0722, LIGA
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: ATCC 700802 / V583
    Synonym: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
11X81Ligand/Ion4-AMINOTHIENO[3,2-C]PYRIDINE-2,7-DICARBOXAMIDE
2NA2Ligand/IonSODIUM ION
3NMN1Ligand/IonBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:87 , LEU A:89 , GLU A:118 , LEU A:119 , LYS A:120 , ILE A:121 , GLU A:175 , TYR A:227 , LYS A:291BINDING SITE FOR RESIDUE 1X8 A 401
2AC2SOFTWARETYR A:25 , SER A:26 , TYR A:29 , TYR A:30 , VAL A:37 , ASP A:39 , TYR A:42 , ASP A:43 , ARG A:158 , HOH A:554 , HOH A:561 , HOH A:581 , HOH A:634BINDING SITE FOR RESIDUE NMN A 402
3AC3SOFTWAREALA A:218 , ARG A:220 , HOH A:535 , HOH A:562 , HOH A:596 , HOH A:627BINDING SITE FOR RESIDUE NA A 403
4AC4SOFTWAREGLU A:276 , SER A:279 , HOH A:543 , HOH A:587BINDING SITE FOR RESIDUE NA A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LH7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LH7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LH7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LH7)

(-) Exons   (0, 0)

(no "Exon" information available for 4LH7)

(-) 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4lh7a_ A: Adenylation domain of NAD+-dependent DNA ligase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.........eee.........ee.hhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhhh.............eeeeeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhh..eeeeeee.........hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lh7 A   2 EQQPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLITPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAFDERVRKAIGKPVAYCCELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVPMRLTEPISVEVRGECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGPMKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNEFALQDELGFTVKAPRWAIAYKFPPEEAE 322
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LH7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LH7)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lh7)
 

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  4lh7
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  6.5.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNLJ_ENTFA | Q837V6: 1ta8 1tae 3ba8 3ba9 3baa 3bab 4eeq 4efb 4efe 4lh6

(-) Related Entries Specified in the PDB File

4lh6 INITIAL HIT FROM VIRTUAL SCREEN