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(-) Description

Title :  DNA LIGASE A IN COMPLEX WITH INHIBITOR
 
Authors :  L. Prade, R. Lange, N. Tidten-Luksch, A. Chambovey
Date :  15 Aug 12  (Deposition) - 10 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Ligase A, Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Surivet, R. Lange, C. Hubschwerlen, W. Keck, J. L. Specklin, D. Ritz, D. Bur, H. Locher, P. Seiler, D. S. Strasser, L. Prade, C. Kohl, C. Schmitt, G. Chapoux, E. Ilhan, N. Ekambaram, A. Athanasiou, A. Knezevic, D. Sabato, A. Chambovey, M. Gaertner, M. Enderlin, M. Boehme, V. Sippel, P. Wyss
Structure-Guided Design, Synthesis And Biological Evaluatio Of Novel Dna Ligase Inhibitors With In Vitro And In Vivo Anti-Staphylococcal Activity.
Bioorg. Med. Chem. Lett. V. 22 6705 2012
PubMed-ID: 23006603  |  Reference-DOI: 10.1016/J.BMCL.2012.08.094

(-) Compounds

Molecule 1 - DNA LIGASE
    Chains: A, B
    EC Number: 6.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LIGA, SPP_1122
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 488223
    Strain: P1031
    Synonym: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD(+)]

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
10XT2Ligand/Ion7-METHOXY-6-METHYLPTERIDINE-2,4-DIAMINE
2NMN1Ligand/IonBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:224 , ASP A:225 , LYS A:229 , LEU B:157 , ASP B:158BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWARETYR A:77 , LEU A:79 , GLU A:107 , LEU A:108 , TYR A:216 , GLN A:217 , VAL A:276 , LYS A:278 , TRP A:297 , HOH A:505BINDING SITE FOR RESIDUE 0XT A 402
3AC3SOFTWARELEU A:157 , ASP A:158 , ARG B:224 , ASP B:225 , LYS B:229 , HOH B:505BINDING SITE FOR RESIDUE SO4 B 401
4AC4SOFTWARETYR B:77 , LEU B:79 , GLU B:107 , LEU B:108 , LYS B:109 , GLU B:164 , TYR B:216 , LYS B:278 , TRP B:297 , HOH B:510BINDING SITE FOR RESIDUE 0XT B 402
5AC5SOFTWAREASP B:53 , LYS B:121 , GLY B:122 , THR B:152 , LEU B:153 , PRO B:154 , GLU B:155 , GLU B:156BINDING SITE FOR RESIDUE NMN B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GLW)

(-) 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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4glwa_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhh...hhhhhh........eeee.........ee.hhhhhhhhhhhhh.......eeeeeee..eeeeeeee..eeeeeee.....eeeehhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhhh..eeeeeee.......hhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4glw A   2 NKRMNERELVELETAYPEQVLADSPTHRVGGKVLDGFEKYSHQYPLYSLQDAFSREELDAFDARVRKEVAHPTYICELKIDGLSISLTYEKGILVAGVTRGDGSIGENITENLKRVKDIPLTLPEELDITVRGECYMPRASFDQVNQARQENGEPEFANPRNAAAGTLRQLDTAVVAKRNLATFLYQEASPSTRDSQEKGLKYLEQLGFVVNPKRILAENIDEIWNFIQEVGQERENLPYDIDGVVIKVNDLASQEELGFTVKAPKWAVAYKFPA 305
                                 || 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
                                 7|                                                                                                                                                                                                                                                                            
                                 37                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4glwb_ B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhh.........eee.........ee.hhhhhhhhhhhhhh......eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhh..eeeeeee.......hhhhhhhhhhhh........eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4glw B   2 NKRMNELVALLNYRELVELETAYPEQVLADSPTHRVGGKVLDGFEKYSHQYPLYSLQDAFSREELDAFDARVRKEVAHPTYICELKIDGLSISLTYEKGILVAGVTRGDGSIGENITENLKRVKDIPLTLPEELDITVRGECYMPRASFDQVNQARQENGEPEFANPRNAAAGTLRQLDTAVVAKRNLATFLYQEASPSTRDSQEKGLKYLEQLGFVVNPKRILAENIDEIWNFIQEVGQERENLPYDIDGVVIKVNDLASQEELGFTVKAPKWAVAYKFP 304
                                    11 ||     43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 
                                      13|                                                                                                                                                                                                                                                                            
                                       36
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  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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

3baa STRUCTURAL BASIS FOR THE INHIBITION OF BACTERIAL NAD+ DEPENDENT DNA LIGASE
4glx