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 :  SELF-ASSEMBLY OF SPIDER SILK PROTEINS IS CONTROLLED BY A PH-SENSITIVE RELAY
 
Authors :  G. Askarieh, H. Hedhammar, K. Nordling, A. Rising, J. Johansson, S. D. K A. Saenz, C. Casals
Date :  11 Feb 10  (Deposition) - 12 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dragline Spider Silk, Self-Assembly, Ph-Dependence, Nt D40N/E84Q Double-Mutant, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Askarieh, M. Hedhammar, K. Nordling, A. Saenz, C. Casals, A. Rising, J. Johansson, S. D. Knight
Self-Assembly Of Spider Silk Proteins Is Controlled By A Ph-Sensitive Relay.
Nature V. 465 236 2010
PubMed-ID: 20463740  |  Reference-DOI: 10.1038/NATURE08962

(-) Compounds

Molecule 1 - MAJOR AMPULLATE SPIDROIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN
    Gene: MASP1
    Mutation: YES
    Organism Scientific: EUPROSTHENOPS AUSTRALIS
    Organism Taxid: 332052

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:51 , SER A:54 , LEU A:55 , SER B:47 , GLN B:50BINDING SITE FOR RESIDUE EDO A 1397
2AC2SOFTWAREGLY A:110 , ALA B:56BINDING SITE FOR RESIDUE EDO B 1397
3AC3SOFTWARESER B:29 , MET B:30 , PRO B:31 , THR B:92 , SER B:95 , SER B:96 , SER B:99 , HOH B:143BINDING SITE FOR RESIDUE PGE B 138

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LRD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LRD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LRD)

(-) 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:129
 aligned with Q05H60_9ARAC | Q05H60 from UniProtKB/TrEMBL  Length:394

    Alignment length:129
                                    34        44        54        64        74        84        94       104       114       124       134       144         
         Q05H60_9ARAC    25 HTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDDMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASEEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFINEITQLVSMFAQAGMND 153
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrd A   6 HTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDNMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASQEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFINEITQLVSMFAQAGMND 134
                                    15        25        35        45        55        65        75        85        95       105       115       125         


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with Q05H60_9ARAC | Q05H60 from UniProtKB/TrEMBL  Length:394

    Alignment length:126
                                    34        44        54        64        74        84        94       104       114       124       134       144      
         Q05H60_9ARAC    25 HTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDDMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASEEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFINEITQLVSMFAQAG 150
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lrd B   6 HTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDNMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASQEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFINEITQLVSMFAQAG 131
                                    15        25        35        45        55        65        75        85        95       105       115       125
   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 3LRD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LRD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lrd)
 

(-) 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
  3lrd
    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
  Q05H60_9ARAC | Q05H60
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q05H60_9ARAC | Q05H60
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q05H60_9ARAC | Q05H60: 2lpi 2lpj 2lth 3lr2 3lr6 3lr8 4fbs

(-) Related Entries Specified in the PDB File

3lr2 NT WILD-TYPE
3lr6
3lr8