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 LINCOSAMIDE ANTIBIOTIC ADENYLYLTRANSFERASE LNUA, LINCOMYCIN-BOUND
 
Authors :  P. J. Stogios, A. Dong, G. Minasov, E. Evdokimova, O. Egorova, M. Kudrit O. Yim, P. Courvalin, A. Savchenko, W. F. Anderson, Center For Struc Genomics Of Infectious Diseases (Csgid)
Date :  20 Sep 14  (Deposition) - 05 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Antibiotic Resistance, Center For Structural Genomics Of Infectious Diseases (Csgid), Alpha+Beta Structure, Aminoglycoside-2''-Adenylyltransferase Superfamily, Nucleotidyltransferase Superfamily, Transferase, Lincosamide Adenylyltransferase, Lincosamide Antibiotics, Lincomycin, Clindamycin, Adenosine Triphosphate, Intracellular, Transferase- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Stogios
Crystal Structure Of Lincosamide Antibiotic Adenylyltransferase Lnua, Lincomycin Bound
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LINCOSAMIDE RESISTANCE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LINA
    Organism Scientific: STAPHYLOCOCCUS HAEMOLYTICUS
    Organism Taxid: 1283

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
13QB2Ligand/IonLINCOMYCIN
2CL1Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION
4MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:115 , ASN A:116 , HOH A:341 , HOH A:352 , LYS B:155binding site for residue CL A 201
2AC2SOFTWAREASP A:46 , ASP A:48 , MG A:203 , 3QB A:204 , HOH A:466 , HOH A:518binding site for residue MG A 202
3AC3SOFTWAREGLY A:29 , GLY A:30 , ASP A:46 , ASP A:48 , MG A:202 , HOH A:449binding site for residue MG A 203
4AC4SOFTWAREASP A:28 , GLY A:29 , GLY A:30 , ASP A:50 , HIS A:92 , PHE A:119 , GLN A:137 , PHE A:140 , MG A:202 , HOH A:389 , HOH A:466 , TYR B:144binding site for residue 3QB A 204
5AC5SOFTWAREASP B:46 , ASP B:48 , ASP B:90 , 3QB B:203 , HOH B:516 , HOH B:527binding site for residue MG B 201
6AC6SOFTWAREGLY B:29 , GLY B:30 , ASP B:46 , ASP B:48 , HOH B:372 , HOH B:374binding site for residue MG B 202
7AC7SOFTWARETYR A:144 , ASP B:28 , ASP B:48 , ASP B:50 , ARG B:78 , ASP B:90 , HIS B:92 , PHE B:119 , PHE B:140 , MG B:201 , HOH B:414 , HOH B:432 , HOH B:510 , HOH B:516 , HOH B:523binding site for residue 3QB B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WH5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Mse A:75 -Pro A:76
2Mse B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WH5)

(-) Exons   (0, 0)

(no "Exon" information available for 4WH5)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..eeeehhhhhhhhhh.......eeeeeee..hhhhhhhhhhhh..eeeeee...eeeeee...eeeeeeeeee.....eeee.....eeeehhh.eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wh5 A   4 NNVTEKELFYILDLFEHmKVTYWLDGGWGVDVLTGKQQREHRDIDIDFDAQHTQKVIQKLEDIGYKIEVHWmPSRmELKHEEYGYLDIHPINLNDDGSITQANPEGGNYVFQNDWFSETNYKDRKIPCISKEAQLLFHSGYDLTETDHFDIKNLKSIT 161
                                    13       |23        33        43        53        63        73 |   |  83        93       103       113       123       133       143       153        
                                            21-MSE                                                75-MSE                                                                                  
                                                                                                      79-MSE                                                                              


Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeeehhhhhhhhh........eeeeeee..hhhhhhhhhhhh..eeeeee...eeeeee...eeeeeeeeee.....eeee.....eee.hhh.eeeeee..eeeeeehhhhhhhhh.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wh5 B   4 NNVTEKELFYILDLFEHmKVTYWLDGGWGVDVLTGKQQREHRDIDIDFDAQHTQKVIQKLEDIGYKIEVHWmPSRmELKHEEYGYLDIHPINLNDDGSITQANPEGGNYVFQNDWFSETNYKDRKIPCISKEAQLLFHSGYDLTETDHFDIKNLKSIT 161
                                    13       |23        33        43        53        63        73 |   |  83        93       103       113       123       133       143       153        
                                            21-MSE                                                75-MSE                                                                                  
                                                                                                      79-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  (0, 0)

(no "SCOP Domain" information available for 4WH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WH5)

(-) Gene Ontology  (1, 1)

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
    3QB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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
    Mse A:75 - Pro A:76   [ RasMol ]  
    Mse B:75 - Pro B:76   [ 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
  4wh5
    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
  LINA_STAHA | P06107
    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)
  (no 'Enzyme Classificator' available)
    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
  LINA_STAHA | P06107
    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
        LINA_STAHA | P06107: 4fo1

(-) Related Entries Specified in the PDB File

4e8j THIS ENTRY SUPERCEDES 4E8J RELATED ID: IDP91779 RELATED DB: TARGETTRACK
4fo1