Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF NAD KINASE V98S MUTANT FROM LISTERIA MONOCYTOGENES
 
Authors :  G. Poncet-Montange, L. Assairi, M. Gelin, S. Pochet, G. Labesse
Date :  01 Nov 15  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Gram-Positive Nad Kinase, Allostery, Citrate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Poncet-Montange, L. Assairi, M. Gelin, S. Pochet, G. Labesse
Crystal Structure Of Nad Kinase 1 From Listeria Monocytogenes: V98S Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NAD KINASE 1
    Chains: A
    EC Number: 2.7.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLA15.3.3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NADK1, LMO0968
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Synonym: ATP-DEPENDENT NAD KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:44 , ASP A:45 , GLY A:46 , HIS A:71 , PHE A:74 , TYR A:75 , ASN A:122 , GLU A:123 , ASP A:150 , SER A:158 , THR A:161 , ALA A:162 , TYR A:163 , SER A:166 , ALA A:185 , ILE A:187 , ASP A:222 , HIS A:223 , HOH A:447 , HOH A:535binding site for residue NAP A 301
2AC2SOFTWARETYR A:100 , HIS A:173 , ARG A:247 , PHE A:251 , PRO A:252 , PHE A:253 , ARG A:256 , HOH A:402 , HOH A:417 , HOH A:442 , HOH A:518binding site for residue CIT A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:76 -Asp A:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EJH)

(-) Sequences/Alignments

Asymmetric 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhh....ee......eeeeeehhhhhhhhhhhh.......eeeeee..........hhhhhhhhhhhhhhh..eeeeeeeeeeeee...eeeee..eeeeee....eeeeeee..eeeeeeee.eeeee.hhhhhhhhhhh..........eeeeeee..............eeee....eeeee.....eeeee..eeeee....eeeeeeeeeeeeeee....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ejh A   1 MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLSAFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKSSYPLLKTTVKYKEATYLALNESTVKSSGGPFVVDVVINDIHFERFRGDGLCMSTPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHHVVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWRRVHDSFIE 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 5EJH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:76 - Asp A:77   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5ejh
    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 5dhq 5dhr 5dhs 5dht 5dhu 5ejf 5ejg 5eji

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5EJH)