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 :  THE CRYSTAL STRUCTURE OF A PUTATIVE HEMOLYSIN FROM LACTOCOCCUS LACTIS
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  01 Sep 10  (Deposition) - 13 Oct 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Sgx, Psi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of A Putative Hemolysin From Lactococcus Lactis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE HEMOLYSIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC - PSGX3 (BC)
    Expression System Strain: BL21 (DE3) - CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: L814, L81441, LL0858, YIIB
    Organism Common: STREPTOCOCCUS LACTIS
    Organism Scientific: LACTOCOCCUS LACTIS SUBSP. LACTIS
    Organism Taxid: 1360
    Strain: LACTIS (LL)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:33 , LEU A:34 , ARG A:35 , TYR A:36 , SER A:38 , ARG A:39 , GLN A:237 , HOH A:278 , HOH A:372BINDING SITE FOR RESIDUE GOL A 2
2AC2SOFTWARESER A:38 , GLY A:40 , SER A:65 , SER A:66 , THR A:67 , GLY A:68 , GLY A:69 , HOH A:265 , HOH A:336BINDING SITE FOR RESIDUE SO4 A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OPN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OPN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OPN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OPN)

(-) Exons   (0, 0)

(no "Exon" information available for 3OPN)

(-) 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:208
 aligned with Q9CH80_LACLA | Q9CH80 from UniProtKB/TrEMBL  Length:243

    Alignment length:209
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
         Q9CH80_LACLA    33 KLRYVSRGGLKLEKALKEFHLEINGKTCLDIGSSTGGFTDVMLQNGAKLVYALDVGTNQLAWKIRSDERVVVMEQFNFRNAVLADFEQGRPSFTSIDVSFISLDLILPPLYEILEKNGEVAALIKPQFEAGREQVGKNGIIRDPKVHQMTIEKVLKTATQLGFSVKGLTFSPIKGGAGNVEFLVHLLKDGKAEIAQQVNIESVLQKESE 241
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---FtsJ-3opnA01 A:36-220                                                                                                                                                                    --------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.......eeeee....hhhhhhhhhh...eeeee.......hhhhhh...eeee...hhhhhhhhhh......eeee.....hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh-.....hhhhhhhhhhhhhhhhhhhh.eeeeeee...........eeeeee...........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3opn A  33 KLRYVSRGGLKLEKALKEFHLEINGKTCLDIGSSTGGFTDVmLQNGAKLVYALDVGTNQLAWKIRSDERVVVmEQFNFRNAVLADFEQGRPSFTSIDVSFISLDLILPPLYEILEKNGEVAALIKPQFEAGREQVG-NGIIRDPKVHQmTIEKVLKTATQLGFSVKGLTFSPIKGGAGNVEFLVHLLKDGKAEIAQQVNIESVLQKESE 241
                                    42        52        62        72 |      82        92       102  |    112       122       132       142       152       162     | 172       182       192       202       212       222       232         
                                                                    74-MSE                        105-MSE                                                        168 |        181-MSE                                                        
                                                                                                                                                                   170
   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 3OPN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OPN)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9CH80_LACLA | Q9CH80)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3opn)
 

(-) 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
  3opn
    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
  Q9CH80_LACLA | Q9CH80
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q9CH80_LACLA | Q9CH80
    Protein Disorder Prediction: DisEMBL | 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 3OPN)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OPN)