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(-) Description

Title :  CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN COMPLEX WITH A NOVEL INHIBITOR
 
Authors :  M. Gelin, J. Paoletti, L. Assairi, V. Huteau, S. Pochet, G. Labesse
Date :  31 Aug 15  (Deposition) - 14 Sep 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetrameric Nad Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Paoletti, L. Assairi, M. Gelin, V. Huteau, M. A. Nahori, O. Dussurget, G. Labesse, S. Pochet
8-Thioalkyl-Adenosine Derivatives Inhibit Listeria Monocytogenes Nad Kinase Through A Novel Binding Mode.
Eur. J. Med. Chem. V. 124 1041 2016
PubMed-ID: 27783975  |  Reference-DOI: 10.1016/J.EJMECH.2016.10.033

(-) Compounds

Molecule 1 - NAD KINASE 1
    Chains: A, B, C, D
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NADK1, LMO0968
    Organism Scientific: LISTERIA MONOCYTOGENES SEROVAR 1/2A (STRAIN ATCC BAA-679 / EGD-E)
    Organism Taxid: 169963
    Strain: ATCC BAA-679 / EGD-E
    Synonym: ATP-DEPENDENT NAD KINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
15AJ4Ligand/Ion5'-AZIDO-8-[(2-{[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]-5'-DEOXYADENOSINE
2CIT2Ligand/IonCITRIC ACID
3GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:98 , TYR A:100 , HIS A:173 , PHE A:251 , PRO A:252 , PHE A:253 , ARG A:256 , HOH A:406binding site for residue CIT A 301
2AC2SOFTWAREASN A:122 , GLU A:123 , ALA A:162 , TYR A:163 , SER A:166 , HIS A:223 , HOH A:413 , GLY C:131 , PRO C:132 , ARG C:148 , GLY C:149 , ASP C:150 , ALA C:185binding site for residue 5AJ A 302
3AC3SOFTWAREVAL B:98 , TYR B:100 , HIS B:173 , PRO B:252 , PHE B:253 , ARG B:256 , HOH B:411binding site for residue CIT B 301
4AC4SOFTWAREASN B:122 , GLU B:123 , LYS B:127 , ALA B:162 , TYR B:163 , SER B:166 , ASP B:222 , HIS B:223 , GLY D:131 , PRO D:132 , ARG D:148 , GLY D:149 , ASP D:150 , ALA D:185binding site for residue 5AJ B 302
5AC5SOFTWAREASP A:150 , LYS C:127 , ASP C:150 , LEU C:167binding site for residue GOL C 301
6AC6SOFTWAREGLY A:131 , PRO A:132 , ARG A:148 , GLY A:149 , ASP A:150 , ALA A:185 , GLY C:46 , LEU C:49 , ASN C:122 , GLU C:123 , ALA C:162 , TYR C:163 , SER C:166 , ASP C:222binding site for residue 5AJ C 302
7AC7SOFTWAREGLY B:131 , ARG B:148 , GLY B:149 , ASP B:150 , ALA B:185 , GLY D:46 , ASN D:122 , GLU D:123 , ALA D:162 , TYR D:163 , SER D:166 , HIS D:223binding site for residue 5AJ D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DHR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DHR)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhh....ee......eeeeeehhhhhhhhhhhh..hhhh.eeeeee..........hhhhhhhhhhhhhhh..eeeeeeeeeeeeee.....eeeee..eeeeee....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee.....eeeeeee..............eeee....eeeee.....eeeee..eeeee..eeeeeeeeeeeeeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhr A   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGIKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIED 264
                                    10        20        30        40        50        60        70        80        90       100       110||     121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
                                                                                                                                        111|                                                                                                                                                       
                                                                                                                                         113                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhhhhh..........eeeeeehhhhhhhhhhhh.......eeeeee..........hhhhhhhhhhhhhh...eeeeeeeeeeeee...eeeee..eeeeeee.eeeeeeee...eeeeeeeeeeeee......hhhhhh...ee......eeeeee..............eee.....eeeee.....eeeee..ee.......eeeeeeeeeeeeeee....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhr B   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYKEATYLALNESTVKSSGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIEDLEH 267
                                    10        20        30        40        50        60        70        80        90       100       114       124    || 135       145       155       165       175       185       195       205       215       225       235       245       255       265  
                                                                                                                                      109|            129|                                                                                                                                        
                                                                                                                                       114             131                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhh...ee......eeeeeehhhhhhhhhhhh..hhhh.eeeeee..........hhhhhhhhhhhhh...eeeeeeeeeeeeee...eeeeee..eeeee.....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee......eeeeee..............eee.....eeeee.....eeeee..eeeee..eeeeeeeeeeeeeeeee....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhr C   1 MKYMITSKGDEKSDLLRLNMIAGFGYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAGEYQKVSYPLLKTTVKYGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
                                    10        20    ||  31        41        51        61        71        81        91|      102       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
                                                   25|                                                              91|              110|                                                                                                                                                      
                                                    27                                                               93               113                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhh...hhhh.eeeeee.......eee...hhhhhhhhhhhh..eeeeeeeeeeeee...eeeee..eeeeee....eeeeeee..eeeeeeee.eeeee......hhhhhh...ee......eeeeee..............eee.....eeeee.....eeeee..eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhr D   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
                                    10        20        30        40        50        60        70        80        90       100       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
                                                                                                                                      109|                                                                                                                                                     
                                                                                                                                       114
   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 5DHR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5dhr
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 Related Entries

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

UniProtKB/Swiss-Prot
        NADK1_LISMO | Q8Y8D7: 2i1w 2i29 2i2a 2i2b 2i2c 2i2d 2i2f 2q5f 3v7u 3v7w 3v7y 3v80 3v8m 3v8n 3v8p 3v8q 3v8r 4dy6 5dhp 5dhq 5dhs 5dht 5dhu 5ejf 5ejg 5ejh 5eji

(-) Related Entries Specified in the PDB File

5dhp 5dhq 5dhs 5dht 5dhu