Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUTATIVE TETRAACYLDISACCHARIDE-1-P 4-KINASE FROM CHROMOBACTERIUM VIOLACEUM. NESG TARGET CVR39.
 
Authors :  S. M. Vorobiev, M. Abashidze, J. Seetharaman, C. X. Chen, M. Jiang, K. Cu L. C. Ma, R. Xiao, T. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northe Structural Genomics Consortium (Nesg)
Date :  22 Jun 06  (Deposition) - 22 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Tetraacyldisaccharide-1-P 4-Kinase, Lpxk, Lipid A Biosynthesis, Nesg, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Vorobiev, M Abashidze, J. Seetharaman, C. X. Chen, M. Jiang, K. Cunningham, L. C. Ma, R. Xiao, T. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Putative Tetraacyldisaccharide-1-P 4-Kinase From Chromobacterium Violaceum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TETRAACYLDISACCHARIDE-1-P 4-KINASE
    ChainsA, B
    EC Number2.7.1.130
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)+ MAGIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCV_3345
    Organism ScientificCHROMOBACTERIUM VIOLACEUM
    Organism Taxid243365
    StrainATCC 12472

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:11 , CYS B:14 , CYS B:29 , ASP B:32BINDING SITE FOR RESIDUE ZN B 101
2AC2SOFTWARECYS A:11 , CYS A:14 , CYS A:29 , ASP A:32BINDING SITE FOR RESIDUE ZN A 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HF1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HF1)

(-) Exons   (0, 0)

(no "Exon" information available for 2HF1)

(-) 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:61
 aligned with Y3345_CHRVO | Q7NSS5 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:61
                                                                                     60  
                                    11        21        31        41        51        |- 
           Y3345_CHRVO    2 DAKFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPMMLESEARELAPEEEVK--  -
               SCOP domains d2hf1a1 A:2-60 Hypothetical protein CV3345                 -- SCOP domains
               CATH domains ------2hf1A01 A:8-62  [code=2.20.25.10, no name defined]      CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..........eee....eeee....eeeeee..ee..hhhhhee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  2hf1 A  2 DAKFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPmmLESEARELAPEEEVKLE 62
                                    11        21        31        41  ||    51        61 
                                                                     44-MSE              
                                                                      45-MSE             

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with Y3345_CHRVO | Q7NSS5 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:59
                                                                                   60  
                                    13        23        33        43        53      |  
           Y3345_CHRVO    4 KFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPMMLESEARELAPEEEVK--  -
               SCOP domains d2hf1b_ B: Hypothetical protein CV3345                      SCOP domains
               CATH domains ----2hf1B01 B:8-62  [code=2.20.25.10, no name defined]      CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........eee....eeee....eeeeee..ee..hhhhhee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  2hf1 B  4 KFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPmmLESEARELAPEEEVKLE 62
                                    13        23        33        43||      53         
                                                                   44-MSE              
                                                                    45-MSE             

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HF1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2HF1)

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hf1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2hf1
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Y3345_CHRVO | Q7NSS5
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.130
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Y3345_CHRVO | Q7NSS5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2HF1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2HF1)