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 :  ROLE OF THE BIRADICAL INTERMEDIATE OBSERVED DURING THE TURNOVER OF SLAC: A TWO-DOMAIN LACCASE FROM STREPTOMYCES COELICOLOR
 
Authors :  I. Nederlof, A. Gupta, G. W. Canters
Date :  04 Sep 12  (Deposition) - 19 Sep 12  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Two-Domain Laccase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gupta, I. Nederlof, S. Sottini, A. W. Tepper, E. J. Groenen, E. A. Thomassen, G. W. Canters
Involvement Of Tyr108 In The Enzyme Mechanism Of The Small Laccase From Streptomyces Coelicolor
J. Am. Chem. Soc. V. 134 18213 2012
PubMed-ID: 23094962  |  Reference-DOI: 10.1021/JA3088604

(-) Compounds

Molecule 1 - PUTATIVE COPPER OXIDASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 38-316
    Gene: SCO6712
    Mutation: YES
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 100226
    Strain: A3(2)
    Synonym: SMALL LACCASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric/Biological Unit (3, 25)
No.NameCountTypeFull Name
1CU12Ligand/IonCOPPER (II) ION
2O3Ligand/IonOXYGEN ATOM
3PG410Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:231 , CYS A:288 , HIS A:293BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:236 , HIS A:287 , CU A:403 , HIS C:158 , O C:402BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:234 , HIS A:236 , CU A:402 , HIS C:102 , HIS C:104 , CU C:401 , O C:402BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWARELYS A:136 , ARG A:146 , PG4 A:408 , HOH A:563BINDING SITE FOR RESIDUE PG4 A 404
05AC5SOFTWAREHIS A:104 , HIS A:156 , CU A:406 , O A:407 , HIS B:289BINDING SITE FOR RESIDUE CU A 405
06AC6SOFTWAREHIS A:102 , HIS A:104 , CU A:405 , O A:407 , HIS B:234 , HIS B:236BINDING SITE FOR RESIDUE CU A 406
07AC7SOFTWAREHIS A:102 , HIS A:156 , HIS A:158 , CU A:405 , CU A:406 , HOH A:533 , HIS B:234 , HIS B:236 , HIS B:287 , HIS B:289 , CU B:402BINDING SITE FOR RESIDUE O A 407
08AC8SOFTWAREGLY A:84 , ASP A:107 , ARG A:133 , THR A:134 , HIS A:135 , LYS A:136 , ARG A:146 , PG4 A:404 , GLY B:278 , HOH B:524BINDING SITE FOR RESIDUE PG4 A 408
09AC9SOFTWAREARG A:49 , LEU A:51 , LEU A:78 , GLU A:80BINDING SITE FOR RESIDUE PG4 A 409
10BC1SOFTWAREHIS B:231 , CYS B:288 , HIS B:293 , MET B:298BINDING SITE FOR RESIDUE CU B 401
11BC2SOFTWAREHIS A:158 , O A:407 , HIS B:236 , HIS B:287BINDING SITE FOR RESIDUE CU B 402
12BC3SOFTWARELYS B:136 , ARG B:146 , GLU C:277BINDING SITE FOR RESIDUE PG4 B 403
13BC4SOFTWAREGLN B:62 , ALA B:72 , VAL B:74 , ASN B:202 , LYS B:204 , HOH C:599BINDING SITE FOR RESIDUE PG4 B 404
14BC5SOFTWAREHIS B:104 , HIS B:156 , O B:406 , HIS C:289 , CU C:405BINDING SITE FOR RESIDUE CU B 405
15BC6SOFTWAREHIS B:102 , HIS B:156 , HIS B:158 , CU B:405 , HOH B:536 , HIS C:234 , HIS C:236 , HIS C:287 , HIS C:289 , CU C:404 , CU C:405BINDING SITE FOR RESIDUE O B 406
16BC7SOFTWARELEU B:78 , GLU B:80BINDING SITE FOR RESIDUE PG4 B 407
17BC8SOFTWAREHIS A:289 , CU A:403 , HIS C:102 , HIS C:104 , HIS C:156 , O C:402BINDING SITE FOR RESIDUE CU C 401
18BC9SOFTWAREHIS A:236 , HIS A:289 , CU A:402 , CU A:403 , HIS C:102 , HIS C:156 , HIS C:158 , CU C:401BINDING SITE FOR RESIDUE O C 402
19CC1SOFTWAREHIS C:231 , CYS C:288 , HIS C:293 , MET C:298BINDING SITE FOR RESIDUE CU C 403
20CC2SOFTWAREHIS B:158 , O B:406 , HOH B:536 , HIS C:236 , HIS C:287 , CU C:405BINDING SITE FOR RESIDUE CU C 404
21CC3SOFTWAREHIS B:102 , HIS B:104 , CU B:405 , O B:406 , HIS C:234 , HIS C:236 , CU C:404BINDING SITE FOR RESIDUE CU C 405
22CC4SOFTWARELYS C:136 , ARG C:139 , ARG C:146 , PG4 C:408BINDING SITE FOR RESIDUE PG4 C 406
23CC5SOFTWAREGLN C:62 , SER C:73 , VAL C:74 , ASN C:202 , HOH C:546BINDING SITE FOR RESIDUE PG4 C 407
24CC6SOFTWAREARG C:133 , THR C:134 , HIS C:135 , LYS C:136 , ARG C:146 , PG4 C:406BINDING SITE FOR RESIDUE PG4 C 408
25CC7SOFTWAREARG C:49 , LEU C:78 , ILE C:79 , GLU C:80BINDING SITE FOR RESIDUE PG4 C 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1Gly A:45 -Gly A:46
2Val A:74 -Pro A:75
3Gly A:208 -Pro A:209
4Glu A:315 -Pro A:316
5Gly B:45 -Gly B:46
6Val B:74 -Pro B:75
7Gly B:208 -Pro B:209
8Gly B:313 -Tyr B:314
9Tyr B:314 -Glu B:315
10Gly C:45 -Gly C:46
11Val C:74 -Pro C:75
12Gly C:208 -Pro C:209
13Glu C:315 -Pro C:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GXF)

(-) 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: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..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxf A  38 TARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDFEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGYEP 316
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         


Chain B 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..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxf B  38 TARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDFEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGYEP 316
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307         


Chain C 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..........eeee...eeeeeeeee....eeeee....ee...............ee.eeee....eeeeeee.......eeeeeee.hhhhhhh..eeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxf C  38 TARTAPAGGEVRHLKMYAEKLADGQMGYGFEKGKASVPGPLIEVNEGDTLHIEFTNTMDVRASLHVHGLDFEISSDGTAMNKSDVEPGGTRTYTWRTHKPGRRDDGTWRPGSAGYWHYHDHVVGTEHGTGGIRNGLYGPVIVRRKGDVLPDATHTIVFNDMTINNRKPHTGPDFEATVGDRVEIVMITHGEYYHTFHMHGHRWADNRTGILTGPDDPSRVIDNKITGPADSFGFQIIAGEGVGAGAWMYHCHVQSHSDMGMVGLFLVKKPDGTIPGYEP 316
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   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 4GXF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    O  [ 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 ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:315 - Pro A:316   [ RasMol ]  
    Glu C:315 - Pro C:316   [ RasMol ]  
    Gly A:208 - Pro A:209   [ RasMol ]  
    Gly A:45 - Gly A:46   [ RasMol ]  
    Gly B:208 - Pro B:209   [ RasMol ]  
    Gly B:313 - Tyr B:314   [ RasMol ]  
    Gly B:45 - Gly B:46   [ RasMol ]  
    Gly C:208 - Pro C:209   [ RasMol ]  
    Gly C:45 - Gly C:46   [ RasMol ]  
    Tyr B:314 - Glu B:315   [ RasMol ]  
    Val A:74 - Pro A:75   [ RasMol ]  
    Val B:74 - Pro B:75   [ RasMol ]  
    Val C:74 - Pro C:75   [ RasMol ]  
 

(-) 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
  4gxf
    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
  Q9XAL8_STRCO | Q9XAL8
    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
  Q9XAL8_STRCO | Q9XAL8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9XAL8_STRCO | Q9XAL8: 3cg8 3kw8 4gy4

(-) Related Entries Specified in the PDB File

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