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 :  CRYSTALS OF CROSS-LINKED STABILIZED AND FUNCTIONAL PHYCOBILISOMES: ONLY PHYCOCYANIN RODS CONTRIBUTE TO DIFFRACTION.
 
Authors :  L. David, M. Prado, A. Arteni, D. A. Elmlund, R. E. Blankenship, N. Adir
Date :  14 Oct 13  (Deposition) - 22 Jan 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (6x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Antenna, Glutaraldehyde Cross-Links, Membrane Associated, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. David, M. Prado, A. A. Arteni, D. A. Elmlund, R. E. Blankenship, N. Adir
Structural Studies Show Energy Transfer Within Stabilized Phycobilisomes Independent Of The Mode Of Rod-Core Assembly
Biochim. Biophys. Acta V. 1837 385 2014
PubMed-ID: 24407142  |  Reference-DOI: 10.1016/J.BBABIO.2013.12.014

(-) Compounds

Molecule 1 - C-PHYCOCYANIN ALPHA SUBUNIT
    Chains: A
    Organism Scientific: THERMOSYNECHOCOCCUS VULCANUS
    Organism Taxid: 32053
 
Molecule 2 - C-PHYCOCYANIN BETA SUBUNIT
    Chains: B
    Organism Scientific: THERMOSYNECHOCOCCUS VULCANUS
    Organism Taxid: 32053

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (6x): AB
Biological Unit 2 (2x): AB
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
2MEN1Mod. Amino AcidN-METHYL ASPARAGINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CYC18Ligand/IonPHYCOCYANOBILIN
2MEN6Mod. Amino AcidN-METHYL ASPARAGINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CYC6Ligand/IonPHYCOCYANOBILIN
2MEN2Mod. Amino AcidN-METHYL ASPARAGINE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1CYC3Ligand/IonPHYCOCYANOBILIN
2MEN1Mod. Amino AcidN-METHYL ASPARAGINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:59 , THR A:66 , SER A:72 , GLN A:73 , TYR A:74 , ALA A:75 , GLY A:80 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:90 , TYR A:110 , LEU A:124 , TRP A:128 , TYR A:129 , HOH A:303 , HOH A:304 , HOH A:314 , ARG B:57 , ILE B:67 , TYR B:76 , THR B:77 , ASN B:78 , HOH B:305BINDING SITE FOR RESIDUE CYC A 201
2AC2SOFTWARELEU B:66 , MEN B:72 , ARG B:79 , ARG B:80 , ALA B:83 , CYS B:84 , ARG B:86 , ASP B:87 , MET B:88 , ILE B:90 , TYR B:94 , LEU B:115 , LEU B:122 , THR B:124 , SER B:128 , HOH B:333 , HOH B:334BINDING SITE FOR RESIDUE CYC B 201
3AC3SOFTWARELEU A:24 , ASP A:28 , ARG A:33 , GLN A:147 , ASN B:35 , LEU B:38 , ASP B:39 , ALA B:144 , ASN B:145 , ILE B:150 , THR B:151 , GLY B:153 , CYS B:155 , MET B:159BINDING SITE FOR RESIDUE CYC B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N6S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N6S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N6S)

(-) Exons   (0, 0)

(no "Exon" information available for 4N6S)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains d4n6sa_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4n6s A   1 MKTPITEAIAAADTQGRFLSNTELQAVDGRFKRAVASMEAARALTNNAQSLIDGAAQAVYQKFPYTTTMQGSQYASTPEGKAKCARDIGYYLRMITYCLVAGGTGPMDEYLIAGLSEINSTFDLSPSWYIEALKYIKANHGLTGQAAVEANAYIDYAINALS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      162       172  
                                                                                                                                                                     140|    150|             
                                                                                                                                                                      143     161             


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains d4n6sb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n6s B   1 MLDAFAKVVAQADARGEFLTNAQFDALSNLVKEGNKRLDAVNRITSNASTIVANAARALFAEQPQLIQPGGnAYTNRRMAACLRDMEIILRYVTYAILAGDSSVLDDRCLNGLRETYQALGTPGSSVAVAIQKMKDAAIAIANDPNGITPGDCSALMSEIAGYFDRAAAAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72-MEN                                                                                                
                                                                                                   75
   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 alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N6S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N6S)

(-) Gene Ontology  (4, 8)

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
    CYC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MEN  [ 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 4n6s)
 
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
  4n6s
    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
  Q71RW8_THEVL | Q71RW8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9AM02_THEVL | Q9AM02
    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
  Q71RW8_THEVL | Q71RW8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9AM02_THEVL | Q9AM02
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q71RW8_THEVL | Q71RW8: 1i7y 1on7 3o18 3o2c 4gxe 4gy3
        Q9AM02_THEVL | Q9AM02: 1i7y 1on7 3o18 3o2c 4gxe 4gy3

(-) Related Entries Specified in the PDB File

3o18 SAME PROTEIN
3o2c SAME PROTEIN