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 :  CRYSTAL STRUCTURE OF LACCASE FROM THERMUS THERMOPHILUS HB27
 
Authors :  H. Serrano-Posada, B. Valderrama, E. Rudino-Pinera
Date :  15 Oct 10  (Deposition) - 26 Oct 11  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Multicopper Oxidases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Serrano-Posada, S. Centeno-Leija, S. P. Rojas-Trejo, C. Rodriguez-Almazan, V. Stojanoff, E. Rudino-Pinera
X-Ray-Induced Catalytic Active-Site Reduction Of A Multicopper Oxidase: Structural Insights Into The Proton- Relay Mechanism And O2-Reduction States.
Acta Crystallogr. , Sect. D V. 71 2396 2015
PubMed-ID: 26627648  |  Reference-DOI: 10.1107/S1399004715018714

(-) Compounds

Molecule 1 - LACCASE
    Chains: A
    EC Number: 1.10.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: MATURE FORM, RESIDUES 24-462
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Other Details: THE PRESENCE OF AN ISOLEUCINE AT THE POSITION 53 IS STRONGLY SUPPORTED BY THE ELECTRON DENSITY.
    Strain: HB27

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD10Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4OH1Ligand/IonHYDROXIDE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:393 , CYS A:445 , HIS A:450 , MET A:455BINDING SITE FOR RESIDUE CU A1463
02AC2SOFTWAREHIS A:95 , HIS A:137 , HIS A:396 , HIS A:398 , HIS A:444 , CU A:1482 , OH A:1483BINDING SITE FOR RESIDUE CU A1464
03AC3SOFTWAREHIS A:97 , TRP A:133 , HIS A:135 , HIS A:446 , OH A:1483BINDING SITE FOR RESIDUE CU A1465
04AC4SOFTWAREASP A:248 , LEU A:263 , GLU A:267 , ARG A:268 , TYR A:414 , LYS A:418 , MRD A:1471BINDING SITE FOR RESIDUE MPD A1466
05AC5SOFTWAREGLN A:56 , LEU A:339 , ARG A:436 , HOH A:2073BINDING SITE FOR RESIDUE MRD A1467
06AC6SOFTWAREPRO A:191 , MET A:295 , MET A:355BINDING SITE FOR RESIDUE MRD A1468
07AC7SOFTWARELYS A:104 , THR A:212 , ARG A:280 , HOH A:2537 , HOH A:2539BINDING SITE FOR RESIDUE MRD A1469
08AC8SOFTWAREGLY A:140 , TRP A:194 , ASP A:452 , ARG A:453 , MPD A:1478BINDING SITE FOR RESIDUE MRD A1470
09AC9SOFTWARELEU A:256 , GLU A:260 , LEU A:261 , PRO A:413 , MPD A:1466 , HOH A:2540BINDING SITE FOR RESIDUE MRD A1471
10BC1SOFTWAREGLU A:127 , LEU A:128 , SER A:334 , HOH A:2407 , HOH A:2541BINDING SITE FOR RESIDUE MRD A1472
11BC2SOFTWAREGLU A:257 , ARG A:276 , PRO A:326 , MPD A:1480 , HOH A:2320 , HOH A:2395BINDING SITE FOR RESIDUE MRD A1473
12BC3SOFTWAREPRO A:342 , VAL A:343 , VAL A:344 , THR A:345BINDING SITE FOR RESIDUE MRD A1474
13BC4SOFTWAREPRO A:28 , GLU A:29 , PHE A:67 , ASN A:206 , HOH A:2007 , HOH A:2063 , HOH A:2090 , HOH A:2092 , HOH A:2275 , HOH A:2542 , HOH A:2543BINDING SITE FOR RESIDUE MPD A1475
14BC5SOFTWAREPRO A:25 , SER A:26 , VAL A:214 , GLN A:216 , ASN A:362 , GLN A:364 , HOH A:2279 , HOH A:2280 , HOH A:2544 , HOH A:2545BINDING SITE FOR RESIDUE MPD A1476
15BC6SOFTWARELYS A:31 , LEU A:44 , GLY A:64 , HOH A:2089BINDING SITE FOR RESIDUE MPD A1477
16BC7SOFTWAREPRO A:191 , ARG A:453 , MRD A:1470BINDING SITE FOR RESIDUE MPD A1478
17BC8SOFTWARESER A:26 , GLN A:376 , ALA A:377 , GLN A:378 , HOH A:2002BINDING SITE FOR RESIDUE MRD A1479
18BC9SOFTWAREASP A:239 , HIS A:240 , ARG A:276 , MRD A:1473 , HOH A:2135 , HOH A:2294 , HOH A:2297BINDING SITE FOR RESIDUE MPD A1480
19CC1SOFTWAREPRO A:144 , PRO A:188 , HIS A:189 , TRP A:194 , HOH A:2131 , HOH A:2213 , HOH A:2249 , HOH A:2546 , HOH A:2547 , HOH A:2548BINDING SITE FOR RESIDUE MRD A1481
20CC2SOFTWAREHIS A:95 , HIS A:97 , HIS A:396 , HIS A:398 , CU A:1464 , HOH A:2138BINDING SITE FOR RESIDUE CU A1482
21CC3SOFTWAREHIS A:95 , HIS A:135 , HIS A:137 , HIS A:444 , HIS A:446 , CU A:1464 , CU A:1465 , HOH A:2549BINDING SITE FOR RESIDUE OH A1483

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XU9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:67 -Pro A:68
2Met A:301 -Ala A:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XU9)

(-) Exons   (0, 0)

(no "Exon" information available for 2XU9)

(-) 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:439
 aligned with Q72HW2_THET2 | Q72HW2 from UniProtKB/TrEMBL  Length:462

    Alignment length:439
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453         
         Q72HW2_THET2    24 GPSFPEPKVVRSQGGLLSLKLSATPTPLALAGQRATLLTYGGSFPGPTLRVRPRDTVRLTLENRLPEPTNLHWHGLPISPKVDDPFLEIPPGESWTYEFTVPKELAGTFWYHPHLHGRVAPQLFAGLLGALVVESSLDAIPELREAEEHLLVLKDLALQGGRPAPHTPMDWMNGKEGDLVLVNGALRPTLVAQKATLRLRLLNASNARYYRLALQDHPLYLIAADGGFLEEPLEVSELLLAPGERAEVLVRLRKEGRFLLQALPYDRGAMGMMDMGGMAHAMPQGPSRPETLLYLIAPKNPKPLPLPKALSPFPTLPAPVVTRRLVLTEDMMAARFFINGQVFDHRRVDLKGQAQTVEVWEVENQGDMDHPFHLHVHPFQVLSVGGRPFPYRAWKDVVNLKAGEVARLLVPLREKGRTVFHCHIVEHEDRGMMGVLEVG 462
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee....eeeeeeeeeeeeeee..eeeeeeee.......eeee....eeeeeeee........eee...................eeeeeee......eeeeee.....hhhhhhhh...eeeee.hhhhhhhhhhh.eeeeeeeeee.ee..ee...hhhhhhhh....eeee......eee....eeeeeeee......eeeee....eeeeee..eeeeeeeee..eee....eeeeeee....eeeeeeee......eeee......eeee......eeeeeeee.......................eeeeeeeeee....eeee...........eee....eeeeeeee.....eeeee.....eeeee..ee........eeee....eeeeeee....eeeeeee.hhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xu9 A  24 GPSFPEPKVVRSQGGLLSLKLSATPTPLAIAGQRATLLTYGGSFPGPTLRVRPRDTVRLTLENRLPEPTNLHWHGLPISPKVDDPFLEIPPGESWTYEFTVPKELAGTFWYHPHLHGRVAPQLFAGLLGALVVESSLDAIPELREAEEHLLVLKDLALQGGRPAPHTPMDWMNGKEGDLVLVNGALRPTLVAQKATLRLRLLNASNARYYRLALQDHPLYLIAADGGFLEEPLEVSELLLAPGERAEVLVRLRKEGRFLLQALPYDRGAMGMMDMGGMAHAMPQGPSRPETLLYLIAPKNPKPLPLPKALSPFPTLPAPVVTRRLVLTEDMMAARFFINGQVFDHRRVDLKGQAQTVEVWEVENQGDMDHPFHLHVHPFQVLSVGGRPFPYRAWKDVVNLKAGEVARLLVPLREKGRTVFHCHIVEHEDRGMMGVLEVG 462
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453
   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 2XU9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XU9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XU9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q72HW2_THET2 | Q72HW2)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0052716    hydroquinone:oxygen oxidoreductase activity    Catalysis of the reaction: 4 hydroquinone + O2 = 4 benzosemiquinone + 4 H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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.

 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 ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OH  [ 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 ]
 
  Cis Peptide Bonds
    Met A:301 - Ala A:302   [ RasMol ]  
    Phe A:67 - Pro A:68   [ 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
  2xu9
    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
  Q72HW2_THET2 | Q72HW2
    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
  Q72HW2_THET2 | Q72HW2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q72HW2_THET2 | Q72HW2: 5jrr 5jx9 5k0d 5k15 5k3k 5k5k 5k7a 5k84
UniProtKB/TrEMBL
        Q72HW2_THET2 | Q72HW2: 2xuw 2xvb 2yae 2yaf 2yah 2yam 2yao 2yap 2yaq 2yar 4ai7 5afa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2XU9)