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 :  CRYSTAL STRUCTURE OF TWO-DOMAIN LACCASE FROM STREPTOMYCES LIVIDANS AC1709 IN COMPLEX WITH AZIDE AFTER 180 MIN SOAKING
 
Authors :  A. Gabdulkhakov, S. Tischenko, L. Yurevich, A. Lisov, A. Leontievsky
Date :  23 Oct 13  (Deposition) - 29 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
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
Crystal Structure Of Two-Domain Laccase From Streptomyces Lividans Ac1709 In Complex With Azide After 180 Min Soaking
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COPPER OXIDASE
    Chains: A
    EC Number: 1.10.3.2
    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  (8, 18)

Asymmetric Unit (8, 18)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
27PE1Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
3AZI6Ligand/IonAZIDE ION
4CU4Ligand/IonCOPPER (II) ION
5GOL2Ligand/IonGLYCEROL
6P6G1Ligand/IonHEXAETHYLENE GLYCOL
7PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
8PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (7, 42)
No.NameCountTypeFull Name
11PE6Ligand/IonPENTAETHYLENE GLYCOL
27PE3Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
3AZI18Ligand/IonAZIDE ION
4CU-1Ligand/IonCOPPER (II) ION
5GOL6Ligand/IonGLYCEROL
6P6G3Ligand/IonHEXAETHYLENE GLYCOL
7PE53Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
8PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
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:531BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:158 , HIS A:236 , HIS A:287 , HOH A:531BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:102 , HIS A:234 , HIS A:236 , AZI A:409 , HOH A:531BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWARETYR A:229 , TYR A:230 , HIS A:293BINDING SITE FOR RESIDUE AZI A 405
06AC6SOFTWARELYS A:69 , GLY A:70 , HIS A:191 , GLU A:212 , ALA A:213 , ASP A:217 , VAL A:219BINDING SITE FOR RESIDUE AZI A 406
07AC7SOFTWARETRP A:240 , ALA A:241 , ASP A:242 , ASN A:243 , ARG A:256 , LYS A:261 , PHE A:269 , GLY A:270BINDING SITE FOR RESIDUE AZI A 407
08AC8SOFTWAREGLY A:148 , ALA A:150 , ARG A:181 , ARG A:244 , VAL A:257 , HOH A:517 , HOH A:550BINDING SITE FOR RESIDUE AZI A 408
09AC9SOFTWAREHIS A:102 , VAL A:103 , TYR A:108 , HIS A:234 , MET A:235 , HIS A:236 , GLY A:237 , HIS A:238 , ASP A:259 , CU A:404 , HOH A:540BINDING SITE FOR RESIDUE AZI A 409
10BC1SOFTWAREHIS A:50 , LYS A:52 , GLU A:90 , HOH A:588BINDING SITE FOR RESIDUE AZI A 410
11BC2SOFTWAREGLU A:109 , ARG A:133 , GLY A:278BINDING SITE FOR RESIDUE PG4 A 411
12BC3SOFTWAREARG A:49 , GLU A:68 , LEU A:78 , GLU A:80BINDING SITE FOR RESIDUE PE5 A 412
13BC4SOFTWAREARG A:40 , LYS A:69 , PRO A:187 , ASP A:188 , VAL A:215 , GLY A:216 , ASP A:217BINDING SITE FOR RESIDUE P6G A 413
14BC5SOFTWAREGLU A:47BINDING SITE FOR RESIDUE GOL A 414
15BC6SOFTWAREASP A:60 , ARG A:170 , ASN A:171 , ASP A:197 , ASN A:202 , LYS A:204 , 1PE A:417 , HOH A:546BINDING SITE FOR RESIDUE 7PE A 416
16BC7SOFTWAREGLN A:62 , SER A:73 , VAL A:74 , PRO A:75 , ASN A:202 , 7PE A:416 , HOH A:523BINDING SITE FOR RESIDUE 1PE A 417
17BC8SOFTWARELYS A:136 , ARG A:139 , ARG A:146BINDING SITE FOR RESIDUE 1PE A 418

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NB7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:45 -Gly A:46
2Val A:74 -Pro A:75
3Gly A:208 -Pro A:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NB7)

(-) Exons   (0, 0)

(no "Exon" information available for 4NB7)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               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
                 4nb7 A  36 GITARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDYEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGYE 315
                                    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       315
   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 4NB7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NB7)

(-) 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    7PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AZI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P6G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PE5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:208 - Pro A:209   [ RasMol ]  
    Gly A:45 - Gly A:46   [ 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
  4nb7
    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)
  1.10.3.2
    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: 4gyb 4naj

(-) Related Entries Specified in the PDB File

4gyb TWO-DOMAIN LACCASE FROM STREPTOMYCES LIVIDANS AT 2.4 A RESOLUTION AC1709
4naj CRYSTAL STRUCTURE OF TWO-DOMAIN LACCASE FROM STREPTOMYCES LIVIDANS AC1709 IN COMPLEX WITH AZIDE AFTER 90 MIN SOAKING