Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) 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 :  2.29
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

 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
15AK4Ligand/Ion8-[(2-{[2-(3-BROMOPHENYL)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:253 , ARG A:256 , HOH A:401binding site for residue CIT A 301
2AC2SOFTWAREASN 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 5AK A 302
3AC3SOFTWAREHOH A:433 , VAL B:98 , TYR B:100 , HIS B:173 , ARG B:247 , PHE B:251 , PRO B:252 , PHE B:253 , ARG B:256 , HOH B:408 , HOH B:419binding site for residue CIT B 301
4AC4SOFTWAREASN B:122 , GLU B:123 , ALA B:162 , TYR B:163 , SER B:166 , HIS B:223 , GLY D:131 , PRO D:132 , ARG D:148 , GLY D:149 , ASP D:150 , ALA D:185binding site for residue 5AK B 302
5AC5SOFTWAREGLY A:131 , PRO A:132 , 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 , HIS C:223binding site for residue 5AK C 301
6AC6SOFTWARELYS A:127 , ASP A:150 , LEU A:167 , ALA A:185 , LYS C:127 , ASP C:150 , LEU C:167 , ALA C:185 , HOH C:430binding site for residue GOL C 302
7AC7SOFTWAREGLY B:131 , PRO B:132 , ARG B:148 , GLY B:149 , ASP B:150 , ALA B:185 , GLU D:123 , ALA D:162 , TYR D:163 , SER D:166 , HIS D:223 , HOH D:419binding site for residue 5AK D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DHQ)

(-) 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.......eeeeee..........hhhhhhhhhhhhhhh..eeeeeeeeeeeeee....eeeeee..eeeeee....eeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhh...ee.....eeeeeeeee............eeee....eeeee.....eeeee..eeeee..eeeeeeeeeeeeeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhq 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhhhh...hhhh.eeeeee..........hhhhhhhhhhhhhh..eeeeeeeeeeee...eeeee..eeeeeee.eeeeeeee...eeeeeeeeeeeee......hhhhhh...ee......eeeeee..............eee.....eeeee.....eeeee...eeee....eeeeeeeeeeeeee.....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhq B   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGQKVSYPLLKTTVKYKEATYLALNESTVKSSGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIEDLEH 267
                                    10        20        30        40        50        60        70        80        90  ||   102      |116       126  ||   137       147       157       167       177       187       197       207       217       227       237       247       257       267
                                                                                                                       93|          109|            129|                                                                                                                                        
                                                                                                                        96           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 .eeeeee..hhhhhhhhhhhhhhhh...ee......eeeeeehhhhhhhhhhhh..hhhh.eeeeee.......eeehhhhhhhhhhhhhh.....eeeeeeeeeeee...eeeeee..eeeeee....eeeeeee...eeeeeee.eeeee.hhhhhhhhhhh...ee......eeeeee..............eee.....eeeee.....eeeee...eeee..eeeeeeeeeeeeeee......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhq 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhh.........eeeeeehhhhhhhhhhh...hhhh.eeeeee..........hhhhhhhhhhhhh....eeeee..eeeeee....eeee..eeeeee....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh...ee......eeeeee..............eee.....eeeee.....eeeee..eeeee....eeeeee....eeeee....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dhq D   1 MKYMITSKGDEKSDLLRLNMIAGEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSYPLLKTTVKYKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 263
                                    10        20  ||    36        46        56        66        76        86        96       106  ||   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
                                                 23|                                                                            109|                                                                                                                                                     
                                                  30                                                                             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 5DHQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5AK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dhq)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5dhq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NADK1_LISMO | Q8Y8D7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.23
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NADK1_LISMO | Q8Y8D7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

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

(-) Related Entries Specified in the PDB File

5dhp 5dhr 5dhs 5dht 5dhu