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 AN IMMUNOREACTIVE 32 KDA ANTIGEN PG49 (PG_0181) FROM PORPHYROMONAS GINGIVALIS W83 AT 1.45 A RESOLUTION (PSI COMMUNITY TARGET, NAKAYAMA)
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Sep 14  (Deposition) - 03 Dec 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Cell Adhesion Protein, Pf16249 Family, Duf4906, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of An Immunoreactive 32 Kda Antigen Pg49 (Pg_0181) From Porphyromonas Gingivalis W83 At 1. 45 A Resolution (Psi Community Target, Nakayama)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - IMMUNOREACTIVE 32 KDA ANTIGEN PG49
    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: PG_0181
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1ACN1Ligand/IonACETONE
2EDO13Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:148 , PHE A:210 , THR A:246 , ACN A:414 , HOH A:634 , HOH A:790BINDING SITE FOR RESIDUE EDO A 401
02AC2SOFTWAREASN A:77 , MSE A:104 , GLU A:108 , ARG A:112BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWARETYR A:81 , TYR A:82 , THR A:89 , EDO A:408 , EDO A:409 , HOH A:612BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREPHE A:194 , GLU A:311 , LEU A:312 , TYR A:313 , ILE A:333 , EDO A:412 , HOH A:695 , HOH A:900BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWARESER A:36 , ILE A:37 , ARG A:38 , MSE A:98 , THR A:254 , HOH A:876BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREARG A:142 , ASP A:151 , ALA A:153 , PRO A:155 , HOH A:691 , HOH A:736 , HOH A:897BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREASP A:72 , GLN A:73 , ALA A:109 , GLU A:111BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWARETYR A:67 , LYS A:125 , ASP A:129 , EDO A:403 , HOH A:713 , HOH A:832BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWARETYR A:82 , ILE A:83 , THR A:84 , GLY A:85 , PHE A:88 , PRO A:306 , EDO A:403 , HOH A:737BINDING SITE FOR RESIDUE EDO A 409
10BC1SOFTWARETHR A:139 , LYS A:141 , ILE A:199 , ILE A:200 , TYR A:220 , HOH A:564BINDING SITE FOR RESIDUE EDO A 410
11BC2SOFTWAREARG A:31 , PRO A:198 , GLY A:270 , HOH A:774 , HOH A:891BINDING SITE FOR RESIDUE EDO A 411
12BC3SOFTWAREGLN A:73 , LEU A:312 , TYR A:313 , ARG A:314 , EDO A:404 , HOH A:742BINDING SITE FOR RESIDUE EDO A 412
13BC4SOFTWAREARG A:38 , ASP A:40 , ASP A:41 , ARG A:53 , PRO A:256 , HOH A:598 , HOH A:715 , HOH A:875BINDING SITE FOR RESIDUE EDO A 413
14BC5SOFTWARESER A:149 , TYR A:212 , GLY A:261 , VAL A:278 , EDO A:401 , HOH A:616BINDING SITE FOR RESIDUE ACN A 414

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:149 -Thr A:150
2Ser A:154 -Pro A:155
3Asp A:173 -Asn A:174
4Trp A:239 -Pro A:240
5Ser A:255 -Pro A:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RDB)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeee....eee..hhhhhh...eeeeee.......eeeee...ee..eeeehhh.eeeeeeehhhhheeeeeeee..hhhhhhhhhhh.hhhhhhh.eee..............eeeeeeee.....eeeeeeeee.eeeeeeeeee.hhhh....ee..eeeeeeeeee.ee.eee..........ee.............eee.hhhhh......eeeeee.....eeeeeeeeeee.......eeeeee........hhhhh..eeeeee........eeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rdb A   0 GDRSIEISIRVDDFTKTGERYERNQGSAAERLITNLYLLLFDQSGANPAKYYITGNTFTGGTWLPDDmKVKLDmTQSEAGERKVYVVANVDNAVKTALDAVANESDLQTVKRTTAmPWSTDIASPFLmSGNKTHDFLANRLLDNVPLVRAIAKVELNISLSEKFQIVPIIVNGSLSEFKFRYVNFDKETYVVKPTTKPDNLISSANGVWPQITDWTVWGASLNTSPAPDAGTGYTLDANGKVTALRIVTYLNERDSKGATVEVALPRVDDGTLPPPEFGPELYRLPLPDKILRNHWYKYEVEI 333
                            ||      38        50        60        70        80        90       100   |   110       120       130       140     | 150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
                            ||               47|                                              98-MSE |                                       146-MSE     158-MSE                                                                                                                                                                           
                            0|                50                                                   104-MSE                                                                                                                                                                                                                                 
                            30
   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 4RDB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4RDB)

 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
    ACN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:173 - Asn A:174   [ RasMol ]  
    Ser A:149 - Thr A:150   [ RasMol ]  
    Ser A:154 - Pro A:155   [ RasMol ]  
    Ser A:255 - Pro A:256   [ RasMol ]  
    Trp A:239 - Pro A:240   [ 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
  4rdb
    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
  MFA4_PORGI | Q7MXK0
    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
  MFA4_PORGI | Q7MXK0
    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 4RDB)

(-) Related Entries Specified in the PDB File

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