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 A LIPOPROTEIN, YAEC FAMILY (EF3198) FROM ENTEROCOCCUS FAECALIS V583 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Dec 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nlpa Lipoprotein, Pf03180 Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi- Biology, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Lipoprotein, Yaec Family (Ef3198) From Enterococcus Faecalis V583 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LIPOPROTEIN, YAEC FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EF_3198, I574_00285, NP_816800.1, OO5_00380
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: ATCC 700802 / V583
    Synonym: YAEC FAMILY LIPOPROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION
5ZN5Ligand/IonZINC ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:41 , ASP A:45BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREGLU A:53 , GLU A:120 , HOH A:599 , HOH A:680BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:74 , HIS A:78 , GLU A:80 , GLU A:180BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWAREGLU A:159 , HIS A:227 , ACT A:310 , HOH A:672BINDING SITE FOR RESIDUE ZN A 304
05AC5SOFTWAREASP A:123 , ASP A:126 , PHE A:272 , ACT A:309BINDING SITE FOR RESIDUE ZN A 305
06AC6SOFTWAREGLU A:53 , GLU A:120 , THR A:253 , LYS A:254 , GLU A:255 , HOH A:622BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREALA A:86 , GLN A:87 , HIS A:88 , PHE A:91 , LEU A:230 , HOH A:503 , HOH A:538 , HOH A:576 , HOH A:590BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREVAL A:76 , ASP A:79 , ALA A:81 , ARG A:235 , GLU A:238 , HOH A:551BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREASP A:123 , ASP A:126 , PHE A:272 , ZN A:305 , HOH A:468BINDING SITE FOR RESIDUE ACT A 309
10BC1SOFTWAREGLU A:159 , HIS A:227 , ZN A:304 , HOH A:448 , HOH A:528 , HOH A:672BINDING SITE FOR RESIDUE ACT A 310
11BC2SOFTWAREGLU A:193 , ASP A:195 , HOH A:615 , HOH A:676BINDING SITE FOR RESIDUE NA A 311

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NTL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTL)

(-) 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d4ntla_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh....eeeeeehhhhhhhhhhhh..eeeeeeeee...eee.....hhhhh....eeeee.hhhhhhhhhhhhhhh...ee........hhh.eee.....eeeeehhhhhhhhh....eeeeeehhhhhh....hhhhh.ee.hhhhhhhh.eeeeee.hhh.hhhhhhhhhhh.hhhhhhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntl A  31 DKEITVAVQLESSKDILEIAKKEAEKKGYKINImEVSDNVAYNDAVQHDEADANFAQHQPFmEmFNKEKKADLVAVQPIYYFAGGFYSKEYQDAKDLPENAKVGIPSDPTNEGRALAILNANGVIKLKEGVGFNGTVADVVENPKNITFESIDLLNLAKAYDEKDIAmVFCYPAYLEPAGLTTKDAILLEDKEASKHYALQVVTRKGEKDSEKIKVLKEAmTTKEVAEYIKKNSKGANIPAF 272
                                    40        50        60   |    70        80        90 | |   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250|      260       270  
                                                            64-MSE                      92-MSE                                                                                                   198-MSE                                              251-MSE                 
                                                                                          94-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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ntl)
 
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
  4ntl
    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
  Q82Z74_ENTFA | Q82Z74
    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
  Q82Z74_ENTFA | Q82Z74
    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 4NTL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NTL)