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 BLUE LACCASE FROM TRAMETES TROGII COMPLEXED WITH P-METHYLBENZOATE
 
Authors :  I. Matera, A. Gullotto, M. Ferraroni, S. Tilli, F. Briganti, A. Scozzaf
Date :  20 Jul 06  (Deposition) - 11 Sep 07  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Laccase, Oxidoreductase, Lignin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Matera, A. Gullotto, S. Tilli, M. Ferraroni, A. Scozzafava, F. Briganti
Crystal Structure Of The Blue Multicopper Oxidase From The White-Rot Fungus Trametes Trogii Complexed With P-Toluate
Inorg. Chim. Acta. V. 361 4129 2008
PubMed: search  |  Reference-DOI: 10.1016/J.ICA.2008.03.091

(-) Compounds

Molecule 1 - LACCASE
    Chains: A
    EC Number: 1.10.3.2
    Organism Scientific: FUNALIA TROGII
    Organism Taxid: 76130
    Strain: 201 (DSM11919)
    Synonym: BLUE LACCASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
14MA1Ligand/Ion4-METHYLBENZOIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA3Ligand/IonCALCIUM ION
4CBS2Ligand/IonDI(N-ACETYL-D-GLUCOSAMINE)
5CU4Ligand/IonCOPPER (II) ION
6GOL3Ligand/IonGLYCEROL
7MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:22 , GLN A:23 , ASN A:54 , MET A:57 , HIS A:153 , LEU A:154 , ALA A:155 , VAL A:158 , ASN A:248 , BMA A:498 , HOH A:3100 , HOH A:3319 , HOH A:3497 , HOH A:3538 , HOH A:3539 , HOH A:3540 , HOH A:3542 , HOH A:3546BINDING SITE FOR RESIDUE CBS A 497
02AC2SOFTWARECBS A:497 , MAN A:499 , HOH A:3319 , HOH A:3545BINDING SITE FOR RESIDUE BMA A 498
03AC3SOFTWAREBMA A:498 , HOH A:3543 , HOH A:3548BINDING SITE FOR RESIDUE MAN A 499
04AC4SOFTWAREALA A:324 , ASN A:326 , SER A:382 , ASN A:433 , HOH A:3108 , HOH A:3266 , HOH A:3321 , HOH A:3333 , HOH A:3339 , HOH A:3439 , HOH A:3460 , HOH A:3463 , HOH A:3506 , HOH A:3526 , HOH A:3527BINDING SITE FOR RESIDUE CBS A 1006
05AC5SOFTWAREHIS A:394 , CYS A:450 , ILE A:452 , HIS A:455BINDING SITE FOR RESIDUE CU A 1497
06AC6SOFTWAREHIS A:64 , HIS A:66 , TRP A:107 , HIS A:109 , HIS A:451 , HOH A:3160BINDING SITE FOR RESIDUE CU A 1498
07AC7SOFTWAREHIS A:64 , HIS A:66 , HIS A:397 , HIS A:399 , HOH A:3036BINDING SITE FOR RESIDUE CU A 1499
08AC8SOFTWAREHIS A:111 , HIS A:399 , HIS A:449 , HOH A:3160BINDING SITE FOR RESIDUE CU A 1500
09AC9SOFTWARESER A:143 , THR A:188 , HOH A:3340 , HOH A:3396 , HOH A:3533BINDING SITE FOR RESIDUE CA A 1001
10BC1SOFTWAREALA A:103 , SER A:224 , HOH A:3075 , HOH A:3122 , HOH A:3170 , HOH A:3259BINDING SITE FOR RESIDUE CA A 1002
11BC2SOFTWAREASP A:183 , GLY A:309 , HOH A:3425 , HOH A:3429 , HOH A:3431 , HOH A:3496BINDING SITE FOR RESIDUE CA A 1003
12BC3SOFTWAREVAL A:162 , PHE A:331 , PRO A:390 , GLY A:391 , HIS A:455 , ALA A:473 , HOH A:3225 , HOH A:3298BINDING SITE FOR RESIDUE 4MA A 3001
13BC4SOFTWAREVAL A:15 , SER A:16 , PRO A:17 , PHE A:31 , LEU A:173 , LYS A:228 , HOH A:3128 , HOH A:3216 , HOH A:3273BINDING SITE FOR RESIDUE GOL A 2001
14BC5SOFTWAREALA A:80 , HIS A:111 , SER A:113 , PHE A:447 , LEU A:456 , HOH A:3027 , HOH A:3256 , HOH A:3387 , HOH A:3415BINDING SITE FOR RESIDUE GOL A 2002
15BC6SOFTWAREALA A:14 , LEU A:26 , ASP A:29 , LYS A:228 , PRO A:229 , THR A:231BINDING SITE FOR RESIDUE GOL A 2003

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:85 -A:485
2A:117 -A:204

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:3 -Pro A:4
2Phe A:31 -Pro A:32
3Leu A:365 -Pro A:366
4Phe A:392 -Pro A:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HRG)

(-) 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:496
 aligned with Q9HDQ0_9APHY | Q9HDQ0 from UniProtKB/TrEMBL  Length:517

    Alignment length:496
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511      
         Q9HDQ0_9APHY    22 AIGPVADLTISNGAVSPDGFSRQAILVNDVFPSPLITGNKGDRFQLNVIDNMTNHTMLKSTSIHWHGFFQHGTNWADGPAFVNQCPISTGHAFLYDFQVPDQAGTFWYHSHLSTQYCDGLRGPIVVYDPQDPHKSLYDVDDDSTVITLADWYHLAAKVGSPVPTADATLINGLGRSIDTLNADLAVITVTKGKRYRFRLVSLSCDPNHVFSIDGHSLTVIEADSVNLKPQTVDSIQIFAAQRYSFVLNADQDVGNYWIRALPNSGTRNFDGGVNSAILRYDGAAPVEPTTSQTPSTNPLVESALTTLEGTAAPGSPAPGGVDLALNMAFGFAGGKFTINGASFTPPTVPVLLQILSGAQSAQDLLPSGSVYSLPANADIEISLPATAAAPGFPHPFHLHGHTFAVVRSAGSSTYNYENPVYRDVVSTGSPGDNVTIRFRTDNPGPWFLHCHIDFHLEAGFAVVMAEDIPEVAATNPVPQAWSDLCPTYDALSPDDQ 517
               SCOP domains d2hrga1 A:1-130 automated matches                                                                                                 d2hrga2 A:131-299 automated matches                                                                                                                                      d2hrga3 A:300-496 automated matches                                                                                                                                                                   SCOP domains
               CATH domains 2hrgA01 A:1-132 Cupredoxins -  blue copper proteins                                                                                 2hrgA02 A:133-308 Cupredoxins -  blue copper proteins                                                                                                                           2hrgA03 A:309-496 Cupredoxins -  blue copper proteins                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eeee...eeeeeeee...hhhhh....eeee......hhhhh..............eeeeeee.....eeeeeee...hhhhhh.eeeeeee.....hhhhh...hhh.eeeeeee...............eeee...............eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeeee......hhhhh.eeeeee...................hhhhh..................eeee..eeee..eeee..........hhhhhhhh...hhhhh.....eeee....eeeeeee..........eeee....eeeee.............ee.eee......eeeeeee....eeeeeee.hhhhhhh..eeeeee...hhhhhh..hhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hrg A   1 AIGPVADLTISNGAVSPDGFSRQAILVNDVFPSPLITGNKGDRFQLNVIDNMTNHTMLKSTSIHWHGFFQHGTNWADGPAFVNQCPISTGHAFLYDFQVPDQAGTFWYHSHLSTQYCDGLRGPIVVYDPQDPHKSLYDVDDDSTVITLADWYHLAAKVGSPVPTADATLINGLGRSIDTLNADLAVITVTKGKRYRFRLVSLSCDPNHVFSIDGHSLTVIEADSVNLKPQTVDSIQIFAAQRYSFVLNADQDVGNYWIRALPNSGTRNFDGGVNSAILRYDGAAPVEPTTSQTPSTNPLVESALTTLEGTAAPGSPAPGGVDLALNMAFGFAGGKFTINGASFTPPTVPVLLQILSGAQSAQDLLPSGSVYSLPANADIEISLPATAAAPGFPHPFHLHGHTFAVVRSAGSSTYNYENPVYRDVVSTGSPGDNVTIRFRTDNPGPWFLHCHIDFHLEAGFAVVMAEDIPEVAATNPVPQAWSDLCPTYDALSPDDQ 496
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9HDQ0_9APHY | Q9HDQ0)
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
    4MA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CBS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:3 - Pro A:4   [ RasMol ]  
    Leu A:365 - Pro A:366   [ RasMol ]  
    Phe A:31 - Pro A:32   [ RasMol ]  
    Phe A:392 - Pro A:393   [ 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
  2hrg
    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
  Q9HDQ0_9APHY | Q9HDQ0
    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
  Q9HDQ0_9APHY | Q9HDQ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9HDQ0_9APHY | Q9HDQ0: 2hrh

(-) Related Entries Specified in the PDB File

2hrh