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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 :  2.62
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
    Synonym: ATP-DEPENDENT NAD KINASE, INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 1

 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
15AG4Ligand/Ion5'-AZIDO-5'-DEOXY-8-[(2-{[2-(3-ETHYNYLPHENYL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]ADENOSINE
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:253binding site for residue CIT A 301
2AC2SOFTWARELYS A:127 , ASP A:150 , LYS C:127 , ASP C:150 , TYR C:163binding site for residue GOL A 302
3AC3SOFTWARELEU A:49 , ASN A:122 , GLU A:123 , ALA A:162 , TYR A:163 , SER A:166 , HIS A:223 , GLY C:131 , PRO C:132 , ARG C:148 , GLY C:149 , ASP C:150 , ALA C:185binding site for residue 5AG A 303
4AC4SOFTWAREVAL B:98 , TYR B:100 , HIS B:173 , SER B:175 , PRO B:252 , PHE B:253 , HOH B:403binding site for residue CIT B 301
5AC5SOFTWAREGLU B:123 , ALA B:162 , TYR B:163 , SER B:166 , HIS B:223 , GLY D:131 , PRO D:132 , GLY D:149 , ASP D:150 , ALA D:185binding site for residue 5AG B 302
6AC6SOFTWAREGLY A:131 , ARG A:148 , GLY A:149 , ASP A:150 , ALA A:185 , ASN C:122 , GLU C:123 , ALA C:162 , TYR C:163 , SER C:166 , ASP C:222 , HIS C:223binding site for residue 5AG C 301
7AC7SOFTWAREGLY B:131 , PRO B:132 , ARG B:148 , GLY B:149 , ASP B:150 , ALA B:185 , ASN D:122 , GLU D:123 , ALA D:162 , TYR D:163 , SER D:166 , HIS D:223 , HOH D:418binding site for residue 5AG D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DHS)

(-) 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 (1) ..eeeee..hhhhhhhhhhhhhhh.............eeeeeehhhhhhhhhhhh..hhhh.eeeeee.......---hhhhhhhhhhhhhhh..eeeee..eeeeeee....eeeeee..eeeee.....eeeeeee...eeeeeee.eeeeee.....hhhhhh...........eeeeee..............eee.....eeeee.....eeeee..eeeee..eeeeeeee....eeeee....hhhhhhhhhhh.. Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------eeee---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhs 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 (1) ..eeeee..hhhhhhhhhhhhhhhhhh..........eeeeeehhhhhhhhhhhh..hhhh.eeeeee.......---hhhhhhhhhhhhhhh..eeeee.eeeeeee...eeeee..eeeee....eeeeeee...eeeeeee.eeeeee.....hhhhhh...........eeeeee..............eee.....eeeee.....eeeee....eee....eeeeeee...eeeee....hhhhhhhhhhh..... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------eeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhs 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeee..hhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhh..hhhh.eeeeee.......---hhhhhhhhhhhhhhh..eeeee.eeeeeeee...eeeeee..eeeee.....eeeeeee...eeeeeee.eeeeee.....hhhhhh...........eeeeee..............eee.....eeeee.....eeeee..eeeee..eeeeeeeee...eeeee....hhhhhhhhhhh. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------eeee-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhs C   1 MKYMITSKGDEKSDLLRLNMIAGFGYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYGKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
                                    10        20    ||  31        41        51        61        71        81        91       101       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
                                                   25|                                                                                110|                                                                                                                                                      
                                                    27                                                                                 113                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhh...hhhh.eeeeee..........hhhhhhhhhhhh..eee.eeeeeee..eeeee..eeeee.....eeeeeee...eeeeeee.eeeeee.....hhhhhh...........eeeeee..............eee.....eeeee.....eeeee..eeeee....eeeeeee...eee......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhs D   2 KYMITSKGDEKSDLLRLNMIAGYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKVSYPLLKTTVKKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
                                    11        21 ||     38        48        58        68        78        88  ||   103    || 118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
                                                23|                                                          91|        108|                                                                                                                                                     
                                                 31                                                           97         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 5DHS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5dhs
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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 5dhr 5dht 5dhu 5ejf 5ejg 5ejh 5eji

(-) Related Entries Specified in the PDB File

5dhp 5dhq 5dhr 5dht 5dhu