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 HUMAN B7-H4 IGV-LIKE DOMAIN
 
Authors :  V. Vigdorovich, U. Ramagopal, R. Bhosle, R. Toro, S. G. Nathenson, S. C. York Structural Genomics Research Consortium (Nysgrc), Atoms Animals: The Immune Function Network (Ifn)
Date :  20 Aug 12  (Deposition) - 12 Sep 12  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Immunoglobulin Domain, Glycoprotein, Disulfide Bond, Immunity, Adaptive Immunity, Structural Genomics, Psi-Biology, Protein Structure Initiative, New York Structural Genomics Research Consortium, Nysgrc, Immunoglobulin Variable-Like Domain, Cell Surface, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Jeon, V. Vigdorovich, S. C. Garrett-Thomson, M. Janakiram, U. A. Ramagopal, Y. M. Abadi, J. S. Lee, L. Scandiuzzi, K. C. Ohaegbulam J. M. Chinai, R. Zhao, Y. Yao, Y. Mao, J. A. Sparano, S. C. Almo, X. Zang
Structure And Cancer Immunotherapy Of The B7 Family Member B7X.
Cell Rep V. 9 1089 2014
PubMed-ID: 25437562  |  Reference-DOI: 10.1016/J.CELREP.2014.09.053

(-) Compounds

Molecule 1 - V-SET DOMAIN-CONTAINING T-CELL ACTIVATION INHIBITOR 1
    Chains: A
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Common: FRUIT FLY
    Expression System Plasmid: MODIFIED PMT-BIP-HIS
    Expression System Strain: SCHNEIDER 2 CELL LINE
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: B7-H4, B7H4, B7S1, B7X, UNQ659/PRO1291, VTCN1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: B7H.5, IMMUNE COSTIMULATORY PROTEIN B7-H4, PROTEIN B7S1, T- CELL COSTIMULATORY MOLECULE B7X

 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
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:57 , PHE A:104 , GLN A:107 , ASN A:112 , SER A:114 , LEU A:122 , NAG A:202 , HOH A:322 , HOH A:344 , HOH A:346 , HOH A:372BINDING SITE FOR RESIDUE NAG A 201
2AC2SOFTWARELYS A:73 , PHE A:104 , LEU A:122 , THR A:123 , ALA A:125 , NAG A:201 , BMA A:203 , MAN A:205 , HOH A:322 , HOH A:392BINDING SITE FOR RESIDUE NAG A 202
3AC3SOFTWAREASP A:51 , ILE A:53 , LYS A:73 , GLU A:74 , GLY A:75 , VAL A:76 , MET A:96 , NAG A:202 , MAN A:204 , MAN A:205 , HOH A:312BINDING SITE FOR RESIDUE BMA A 203
4AC4SOFTWAREALA A:45 , ILE A:62 , GLY A:75 , LEU A:77 , ASP A:94 , BMA A:203 , HOH A:345 , HOH A:347 , HOH A:355 , HOH A:356 , HOH A:359 , HOH A:378BINDING SITE FOR RESIDUE MAN A 204
5AC5SOFTWAREILE A:53 , GLU A:74 , PHE A:104 , ARG A:116 , GLY A:126 , THR A:127 , NAG A:202 , BMA A:203 , HOH A:335 , HOH A:360 , HOH A:366 , HOH A:396BINDING SITE FOR RESIDUE MAN A 205

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:56 -A:130

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GOS)

(-) 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:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.eeee....eeeeeee....hhhh.eeeeee.......eeee..ee.....hhhhh..eee...hhhhh...eee...hhhhheeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4gos A  35 HSITVTTVASAGNIGEDGILSCTFEPDIKLSDIVIQWLKEGVLGLVHEFKEGKDELSEQDEMFRGRTAVFADQVIVGNASLRLKNVQLTDAGTYKCYIITSKGKGNANLEYKTGH 149
                                    44        54        64        74        84        94       104       114       124       134       144
   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 4GOS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gos)
 

(-) 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
  4gos
    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
  VTCN1_HUMAN | Q7Z7D3
    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
  VTCN1_HUMAN | Q7Z7D3
    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 4GOS)

(-) Related Entries Specified in the PDB File

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