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 :  TWO-DOMAIN LACCASE FROM STREPTOMYCES LIVIDANS AT 2.4 A RESOLUTION AC1709
 
Authors :  A. Gabdulkhakov, S. Tischenko, L. Yurevich, A. Lisov, A. Leontievsky
Date :  05 Sep 12  (Deposition) - 02 Oct 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Multicopper Blue Protein, Two-Domain Laccase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gabdulkhakov, S. Tischenko, L. Yurevich, A. Lisov, A. Leontievsky
Two-Domain Laccase From Streptomyces Lividans At 2. 4 A Resolution Ac1709
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COPPER OXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSPG_00990
    Organism Scientific: STREPTOMYCES LIVIDANS
    Organism Taxid: 457428
    Strain: TK24
    Synonym: LACCASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CU4Ligand/IonCOPPER (II) ION
3NA1Ligand/IonSODIUM ION
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION
3NA-1Ligand/IonSODIUM ION
4PG46Ligand/IonTETRAETHYLENE GLYCOL
5PGE6Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:231 , CYS A:288 , HIS A:293 , MET A:298BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:104 , HIS A:156 , HIS A:289 , HOH A:512BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:158 , HIS A:236 , HIS A:287 , HOH A:512BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:102 , HIS A:104 , HIS A:234 , HIS A:236 , HOH A:511 , HOH A:512BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWAREARG A:49 , GLU A:80 , PGE A:409 , HOH A:653 , HOH A:654BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWARETHR A:192BINDING SITE FOR RESIDUE CL A 406
07AC7SOFTWAREGLN A:62 , SER A:73 , VAL A:74 , ASN A:202 , PG4 A:410 , HOH A:611BINDING SITE FOR RESIDUE PG4 A 407
08AC8SOFTWARELYS A:136 , ARG A:139 , ARG A:146BINDING SITE FOR RESIDUE PGE A 408
09AC9SOFTWAREARG A:49 , LEU A:78 , GLU A:80 , NA A:405 , HOH A:653 , HOH A:654BINDING SITE FOR RESIDUE PGE A 409
10BC1SOFTWAREARG A:170 , ASN A:171 , ASN A:202 , PG4 A:407 , HOH A:621BINDING SITE FOR RESIDUE PG4 A 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:74 -Pro A:75
2Gly A:208 -Pro A:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GYB)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.....eeee............eeee...eeeeeeee........ee.....hhhhh.............eeeeeee....ee.....ee....eeeeee........hhhhhhhh.eeeeeee........eeeeeeee..ee.........eeeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyb A  36 GITARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDYEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGY 314
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   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 4GYB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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
    Gly A:208 - Pro A:209   [ RasMol ]  
    Val A:74 - Pro A:75   [ 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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4gyb
    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
  D6EFA0_STRLI | D6EFA0
    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
  D6EFA0_STRLI | D6EFA0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D6EFA0_STRLI | D6EFA0: 4naj 4nb7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4GYB)