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
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)

(-) Description

Title :  PLASTOCYANIN VARIANT WITH N-TERMINAL METHIONINE - OPEN STRUCTURE
 
Authors :  P. B. Crowley, P. M. Matias, A. R. Khan
Date :  14 Jan 09  (Deposition) - 27 Oct 09  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Protein Interactions, Transport, Cupredoxin, Self-Assembly, Metal-Binding, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. B. Crowley, P. M. Matias, A. R. Khan, M. Roessle, D. I. Svergun
Metal-Mediated Self-Assembly Of A Beta-Sandwich Protein.
Chemistry V. 15 12672 2009
PubMed-ID: 19834935  |  Reference-DOI: 10.1002/CHEM.200901410

(-) Compounds

Molecule 1 - PLASTOCYANIN
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificPHORMIDIUM LAMINOSUM
    Organism Taxid32059

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CU3Ligand/IonCOPPER (II) ION
2ZN7Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:39 , CYS A:89 , HIS A:92 , MET A:97BINDING SITE FOR RESIDUE CU A 106
02AC2SOFTWAREHIS A:61 , ASP B:44 , ASP B:45BINDING SITE FOR RESIDUE ZN A 107
03AC3SOFTWAREMET A:0 , GLU A:1 , HIS A:24 , ASP A:27BINDING SITE FOR RESIDUE ZN A 108
04AC4SOFTWAREHIS C:39 , CYS C:89 , HIS C:92 , MET C:97BINDING SITE FOR RESIDUE CU B 106
05AC5SOFTWAREASP A:44 , ASP A:45 , HIS C:61BINDING SITE FOR RESIDUE ZN B 107
06AC6SOFTWAREMET C:0 , GLU C:1 , HIS C:24 , ASP C:27BINDING SITE FOR RESIDUE ZN B 108
07AC7SOFTWAREHIS B:39 , CYS B:89 , HIS B:92 , MET B:97BINDING SITE FOR RESIDUE CU C 106
08AC8SOFTWAREHIS B:61 , ASP C:44 , ASP C:45BINDING SITE FOR RESIDUE ZN C 107
09AC9SOFTWAREGLU B:1 , HIS B:24 , ASP B:27BINDING SITE FOR RESIDUE ZN C 108
10BC1SOFTWAREMET B:0BINDING SITE FOR RESIDUE ZN C 109

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W88)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:17 -Pro A:18
2Pro A:37 -Pro A:38
3Glu B:17 -Pro B:18
4Pro B:37 -Pro B:38
5Glu C:17 -Pro C:18
6Pro C:37 -Pro C:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W88)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.PLAS_PHOLA116-131
 
 
  3A:82-97
B:82-97
C:82-97
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.PLAS_PHOLA116-131
 
 
  6A:82-97
B:82-97
C:82-97

(-) Exons   (0, 0)

(no "Exon" information available for 2W88)

(-) 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:106
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:106
                                    43        53        63        73        83        93       103       113       123       133      
           PLAS_PHOLA    34 AETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d2w88a_ A: Plastocyanin                                                                                    SCOP domains
               CATH domains 2w88A00 A:0-105 Cupredoxins -  blue copper proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee..eeee....eeeeee.....eeeee.hhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2w88 A   0 METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                     9        19        29        39        49        59        69        79        89        99      

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:106
                                    43        53        63        73        83        93       103       113       123       133      
           PLAS_PHOLA    34 AETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d2w88b_ B: Plastocyanin                                                                                    SCOP domains
               CATH domains 2w88B00 B:0-105 Cupredoxins -  blue copper proteins                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee..eeee....eeeeee.....eeeee.hhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2w88 B   0 METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                     9        19        29        39        49        59        69        79        89        99      

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with PLAS_PHOLA | Q51883 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:106
                                    43        53        63        73        83        93       103       113       123       133      
           PLAS_PHOLA    34 AETFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 139
               SCOP domains d2w88c_ C: Plastocyanin                                                                                    SCOP domains
               CATH domains 2w88C00 C:0-105 Cupredoxins -  blue copper proteins                                                        CATH domains
           Pfam domains (1) ---Copper-bind-2w88C01 C:3-104                                                                           - Pfam domains (1)
           Pfam domains (2) ---Copper-bind-2w88C02 C:3-104                                                                           - Pfam domains (2)
           Pfam domains (3) ---Copper-bind-2w88C03 C:3-104                                                                           - Pfam domains (3)
         Sec.struct. author ..eeeeee........ee..eeee....eeeeee.....eee..hhhhhhhhhhhhhhhhheeeee.....eeeee.......eeeeee...hhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------COPPER_BLUE     -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2w88 C   0 METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG 105
                                     9        19        29        39        49        59        69        79        89        99      

   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  (1, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PLAS_PHOLA | Q51883)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0042651    thylakoid membrane    The pigmented membrane of any thylakoid.

 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
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:17 - Pro A:18   [ RasMol ]  
    Glu B:17 - Pro B:18   [ RasMol ]  
    Glu C:17 - Pro C:18   [ RasMol ]  
    Pro A:37 - Pro A:38   [ RasMol ]  
    Pro B:37 - Pro B:38   [ RasMol ]  
    Pro C:37 - Pro C:38   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2w88
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLAS_PHOLA | Q51883
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PLAS_PHOLA | Q51883
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLAS_PHOLA | Q518831baw 2q5b 2w8c 3bqv 3cvb 3cvc 3cvd 4r0o

(-) Related Entries Specified in the PDB File

1baw PLASTOCYANIN FROM PHORMIDIUM LAMINOSUM