Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE DISCOBODY: AN ENGINEERED DISCOIDIN DOMAIN FROM FACTOR VIII THAT BINDS V 3 INTEGRIN WITH ANTIBODY-LIKE AFFINITIES
 
Authors :  G. Kym, K. Shi, A. Kamajaya, S. Hamdouche, J. S. Kostecki, T. Wannier, B. P. Nikolovski, S. L. Mayo
Date :  10 Mar 14  (Deposition) - 08 Apr 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Integrin Binding, Integrin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Kym, K. Shi, A. Kamajaya, S. Hamdouche, J. S. Kostecki, T. Wannier, B. Li, P. Nikolovski, S. L. Mayo
The Discobody: An Engineered Discoidin Domain From Factor Viii That Binds V 3 Integrin With Antibody-Like Affinities
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COAGULATION FACTOR VIII
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2190-2351
    Gene: F8, F8C
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIHEMOPHILIC FACTOR, AHF, PROCOAGULANT COMPONENT, FACTOR VIIIA HEAVY CHAIN, 200 KDA ISOFORM, FACTOR VIIIA HEAVY CHAIN, 92 KDA ISOFORM, FACTOR VIII B CHAIN, FACTOR VIIIA LIGHT CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4PT6)

(-) Sites  (0, 0)

(no "Site" information available for 4PT6)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:28 -A:33
2B:28 -B:33

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:129 -Pro A:130
2Arg B:46 -Ser B:47
3Ser B:81 -Ala B:82
4Ala B:82 -Ala B:83
5Asp B:129 -Pro B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PT6)

(-) Exons   (0, 0)

(no "Exon" information available for 4PT6)

(-) 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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee............eee....ee..ee.hhhhh....................eeeeeeeeeeeeeeeee.eee..eeeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pt6 A   4 SCSMPLGMESKAISDAQITASSYACRGDTCWSPSKARLHLQGRSNAWRPQVNNKEWLQVDFQKTMKVTGVTTQGVKSAATSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALRMEVLGCE 158
                                    13        23        33        43        53  ||    64        74        84        94       104       114       124       134       144       154    
                                                                               56|                                                                                                    
                                                                                58                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee............eee....ee..ee.hhhhh.....................eeeeeeeeeeeeeeeee.ee....eeeeeeeeeeee......ee........ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pt6 B   6 SMPLGMESKAISDAQITASSYACRGDTCWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSAATSMYVKEFLISSSQDGHQWTLFFNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALRMEVLGCEA 159
                                    15        25        35        45        55        65        75        85        95       105||     116       126       136       146       156   
                                                                                                                              106|                                                   
                                                                                                                               108
   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 4PT6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PT6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PT6)

(-) Gene Ontology  (21, 21)

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
(no "Ligands, Modified Residues, Ions" information available for 4pt6)
 
  Sites
(no "Sites" information available for 4pt6)
 
  Cis Peptide Bonds
    Ala B:82 - Ala B:83   [ RasMol ]  
    Arg B:46 - Ser B:47   [ RasMol ]  
    Asp A:129 - Pro A:130   [ RasMol ]  
    Asp B:129 - Pro B:130   [ RasMol ]  
    Ser B:81 - Ala B:82   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 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
  4pt6
    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
  FA8_HUMAN | P00451
    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
  FA8_HUMAN | P00451
    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
        FA8_HUMAN | P00451: 1cfg 1d7p 1fac 1iqd 2r7e 3cdz 3hnb 3hny 3hob 3j2q 3j2s 4bdv 4ki5 4xzu 5k8d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PT6)