Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  CRYSTAL STRUCTURE AND THERMODYNAMIC ANALYSIS OF DIAGNOSTIC FAB 106.3 COMPLEXED WITH BNP 5-13 (C10A) REVEAL BASIS OF SELECTIVE MOLECULAR RECOGNITION
 
Authors :  K. L. Longenecker, Q. Ruan, E. H. Fry, S. S. Saldana, S. E. Brophy, P. L. Richardson, S. Y. Tetin
Date :  20 Aug 08  (Deposition) - 07 Jul 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  H,L,P
Biol. Unit 1:  H,L,P  (2x)
Biol. Unit 2:  H,L,P  (1x)
Keywords :  Fab 106. 3, Igg1, Brain Natriuretic Peptide (Bnp), Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Longenecker, Q. Ruan, E. H. Fry, S. C. Saldana, S. E. Brophy, P. L. Richardson, S. Y. Tetin
Crystal Structure And Thermodynamic Analysis Of Diagnostic Mab 106. 3 Complexed With Bnp 5-13 (C10A).
Proteins V. 76 536 2009
PubMed-ID: 19274732  |  Reference-DOI: 10.1002/PROT.22366
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB 106.3 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FAB 106.3 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - BNP PEPTIDE EPITOPE
    Chains: P
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLP
Biological Unit 1 (2x): HLP
Biological Unit 2 (1x): HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3E8U)

(-) Sites  (0, 0)

(no "Site" information available for 3E8U)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:142 -H:197
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Phe H:148 -Pro H:149
2Glu H:150 -Pro H:151
3Trp H:190 -Pro H:191
4Ser L:7 -Pro L:8
5His L:76 -Pro L:77
6Asp L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E8U)

(-) Exons   (0, 0)

(no "Exon" information available for 3E8U)

(-) 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 H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e8uH01 H:1-113 Immunoglobulins                                                                                      3e8uH02 H:114-213 Immunoglobulins                                                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e8u H   1 QIQLVQSGPELRKPGETVKISCKGSGYTFTHYGINWVKQTPSKDLKWMGWINTHTGEPIYADDFKGRFAFSLETSANTAYLQINNLNNGDMGTYFCTRSHRFGLDYWGQGTSVTVSSAKTTPPSVYPLAPGSAASMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKILD 214
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126   ||  141       151       161       171       181       191       201       211   
                                                                              52A                            82A||                                             130|                                                                              
                                                                                                              82B|                                              136                                                                              
                                                                                                               82C                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d3e8ul1 L:1-107 automated matches                                                                              d3e8ul2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------3e8uL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e8u L   1 DNVLTQSPPSLAVSLGQRATISCKASQSVDYNGDSYLNWYQQKPGQPPKFLIYAASNLESGIPARFSGSGSGTDFNLNIHPVEEEDAATYYCQQSNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                     27A|||                                                                                                                                                                                         
                                                      27B||                                                                                                                                                                                         
                                                       27C|                                                                                                                                                                                         
                                                        27D                                                                                                                                                                                         


Chain P from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3e8u P   4 GVQGSGAFGRG  14
                                    13
   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  (2, 2)

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

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E8U)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3E8U)

 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 3e8u)
 
  Sites
(no "Sites" information available for 3e8u)
 
  Cis Peptide Bonds
    Asp L:94 - Pro L:95   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    His L:76 - Pro L:77   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:190 - Pro H:191   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ 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
  3e8u
    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 3E8U)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3E8U)