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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF FABOX108
 
Authors :  J. Ren, J. E. Nettleship, R. J. Owens, Oxford Protein Production Facility (Oppf)
Date :  13 Jun 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Antibody Fragments, Fabs, Transient Expression, Structural Genomics, Oxford Protein Production Facility, Oppf, Immunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Nettleship, J. Ren, N. Rahman, N. S. Berrow, D. Hatherley, A. N. Barclay, R. J. Owens
A Pipeline For The Production Of Antibody Fragments For Structural Studies Using Transient Expression In Hek 293T Cells.
Protein Expr. Purif. V. 62 83 2008
PubMed-ID: 18662785  |  Reference-DOI: 10.1016/J.PEP.2008.06.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FABOX108 LIGHT CHAIN FRAGMENT
    Chains: A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Organ: HUMAN EMBRYONIC KIDNEY CELLS
    Expression System Plasmid: POPING-ET
    Expression System Strain: 293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VL
 
Molecule 2 - FABOX108 HEAVY CHAIN FRAGMENT
    Chains: B, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Organ: HUMAN EMBRYONIC KIDNEY CELLS
    Expression System Plasmid: POPING-ET
    Expression System Strain: 293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VH

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU D:46 , LYS D:65BINDING SITE FOR RESIDUE MG D 456

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:92
2A:137 -A:197
3B:22 -B:96
4B:146 -B:201
5C:23 -C:92
6C:137 -C:197
7D:22 -D:96
8D:146 -D:201

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2His A:80 -Pro A:81
3Tyr A:143 -Pro A:144
4Phe B:152 -Pro B:153
5Glu B:154 -Pro B:155
6Trp B:194 -Pro B:195
7Ser C:7 -Pro C:8
8His C:80 -Pro C:81
9Tyr C:143 -Pro C:144
10Phe D:152 -Pro D:153
11Glu D:154 -Pro D:155
12Trp D:194 -Pro D:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DGG)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains d3dgga1 A:1-110 automated matches                                                                             d3dgga2 A:111-217 automated matches                                                                         SCOP domains
               CATH domains -----3dggA01 A:6-110 Immunoglobulins                                                                          3dggA02 A:111-214 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dgg A   1 DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHSRELLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -----------------------------------------------------------------------------------------------------------------------d3dggb1 B:120-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma               SCOP domains
               CATH domains 3dggB01 B:1-119 Immunoglobulins                                                                                        3dggB02 B:120-216 Immunoglobulins                                                         --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee...eeeeeeeeeee.....eeee....hhh.eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dgg B   1 EVKLQQSGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDDTNYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCAREDYYGSRWGYWGQGTTLTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217  
                                                                                                                                                             132|                                                                               
                                                                                                                                                              140                                                                               


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d3dggc1 C:1-110 automated matches                                                                             d3dggc2 C:111-215 automated matches                                                                       SCOP domains
               CATH domains -----3dggC01 C:6-110 Immunoglobulins                                                                          3dggC02 C:111-214 Immunoglobulins                                                                       - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dgg C   1 DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHSRELLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains -----------------------------------------------------------------------------------------------------------------------d3dggd1 D:120-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                - SCOP domains
               CATH domains 3dggD01 D:1-119 Immunoglobulins                                                                                        3dggD02 D:120-216 Immunoglobulins                                                           ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee......eeeeeee....eeeeeee..hhhhheeeeeee.........ee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhhhhh.eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dgg D   1 EVKLQQSGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDDTNYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCAREDYYGSRWGYWGQGTTLTVSSAKTTPPSVYPLAPGSSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185       195       205       215     
                                                                                                                                                               134|                                                                                
                                                                                                                                                                140
   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  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Homo sapiens. Organism_taxid: 9606. (14)
1a3dggA02A:111-214
1b3dggD02D:120-216
1c3dggB02B:120-216
1d3dggA01A:6-110
1e3dggC02C:111-214
1f3dggC01C:6-110
1g3dggB01B:1-119
1h3dggD01D:1-119

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DGG)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3DGG)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:154 - Pro B:155   [ RasMol ]  
    Glu D:154 - Pro D:155   [ RasMol ]  
    His A:80 - Pro A:81   [ RasMol ]  
    His C:80 - Pro C:81   [ RasMol ]  
    Phe B:152 - Pro B:153   [ RasMol ]  
    Phe D:152 - Pro D:153   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Trp B:194 - Pro B:195   [ RasMol ]  
    Trp D:194 - Pro D:195   [ RasMol ]  
    Tyr A:143 - Pro A:144   [ RasMol ]  
    Tyr C:143 - Pro C:144   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3dgg
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3DGG)

(-) Related Entries Specified in the PDB File

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