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 "COMPACT P-LOOP" LPXK FROM AQUIFEX AEOLICUS IN COMPLEX WITH CHLORIDE AT 2.2 ANGSTROM RESOLUTION
 
Authors :  R. P. Emptage, C. W. Pemble Iv, J. D. York, C. R. H. Raetz, P. Zhou
Date :  18 Jan 13  (Deposition) - 03 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Membrane Protein, Kinase, Lipid A, P-Loop, P-Loop Containing Nucleoside Triphosphate Hydrolase, Disaccharide-1-Phosphate 4'- Kinase, Membrane, Transferase, Lipid Metabolism, Tetraacyldisaccharide 4'-Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Emptage, C. W. Pemble, J. D. York, C. R. Raetz, P. Zhou
Mechanistic Characterization Of The Tetraacyldisaccharide-1-Phosphate 4'-Kinase Lpxk Involved I Lipid A Biosynthesis.
Biochemistry V. 52 2280 2013
PubMed-ID: 23464738  |  Reference-DOI: 10.1021/BI400097Z

(-) Compounds

Molecule 1 - TETRAACYLDISACCHARIDE 4'-KINASE
    Chains: A
    EC Number: 2.7.1.130
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LPXK, AQ_1656
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: LIPID A 4'-KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL4Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:287 , GLU A:289 , HOH A:561 , HOH A:571BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWAREARG A:72 , GLN A:142 , HIS A:143 , HOH A:508 , HOH A:564BINDING SITE FOR RESIDUE EPE A 402
3AC3SOFTWAREASP A:237 , THR A:278 , HOH A:541BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREMET A:56 , ASN A:295BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWARETYR A:315BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWAREASN A:43 , GLY A:48 , GLY A:50 , LYS A:51 , HOH A:501BINDING SITE FOR RESIDUE CL A 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:165 -Pro A:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ITN)

(-) 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:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhhhh....eeeee..........eeeee..ee..hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh..eeeee...........eeeeeehhhhhhh..........hhhhhhhh.eeee...............eeeeeeeeeeee.....eehhhhhh...eeeee...hhhhhhhhhhhh...eeeeee.................eeehhhhhhhhh....eeeeeeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4itn A   4 SSLLPFSYLYEKIINFRNTLYDKGFLKIKKLPVPVISVGNLSVGGSGKTSFVMYLADLLKDKRVCILSRGYKRKSKGTLIVSEYGNLKVSWEEAGDEPYLMAKLLPHVSVVASEDRYKGGLLALEKLSPEVFILDDGFQHRKLHRDLNILLLKKKDLKDRLLPAGNLREPLKEIRRADALVLTYQEVEPFEFFTGKPTFKMFREFCCLLNSDFEEVPFDILKEREVIAFSGLGDNGQFRKVLKNLGIKVKEFMSFPDHYDYSDFTPEEGEIYLTTPKDLIKLQGYENVFALNFKVKLEREEKLKKLIYRIFY 315
                                    13        23        33        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       313
   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 4ITN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ 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 ]
 
  Cis Peptide Bonds
    Leu A:165 - Pro A:166   [ RasMol ]  
 

(-) 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
  4itn
    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
  LPXK_AQUAE | O67572
    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)
  2.7.1.130
    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
  LPXK_AQUAE | O67572
    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
        LPXK_AQUAE | O67572: 4ehw 4ehx 4ehy 4itl 4itm 4lkv

(-) Related Entries Specified in the PDB File

4ehw 4ehx 4ehy