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 FRON THERMUS THERMOPHILUS HB27 (SODIUM NITRATE 1.5 MIN)
 
Authors :  A. Diaz-Vilchis, R. R. Ruiz-Arellano, E. Rosas-Benitez, E. Rudino-Pi
Date :  25 May 16  (Deposition) - 07 Jun 17  (Release) - 07 Jun 17  (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 :  A. Diaz-Vilchis, R. R. Ruiz-Arellano, E. Rosas-Benitez, V. Stojanoff, E. Rudino-Pinera
Preserving Metalic Sites Affected By Radiation Damage: The Cut2 Case In Thermus Thermophilus Multicopper Oxidase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACCASE
    Chains: A
    EC Number: 1.10.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 24-462
    Gene: TT_C1370
    Organism Scientific: THERMUS THERMOPHILUS (STRAIN HB27 / ATCC BAA- 163 / DSM 7039)
    Organism Taxid: 262724
    Strain: HB27 / ATCC BAA-163 / DSM 7039
    Synonym: MULTICOPPER OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1CU3Ligand/IonCOPPER (II) ION
2MPD15Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , HIS A:137 , HIS A:396 , HIS A:398 , HIS A:444binding site for residue CU A 501
02AC2SOFTWAREHIS A:95 , HIS A:97 , TRP A:133 , HIS A:135 , HIS A:446binding site for residue CU A 502
03AC3SOFTWAREHIS A:393 , CYS A:445 , HIS A:450 , MET A:455binding site for residue CU A 503
04AC4SOFTWAREPRO A:342 , VAL A:343 , VAL A:344 , THR A:345 , HOH A:603binding site for residue MPD A 504
05AC5SOFTWAREARG A:276 , MPD A:516 , HOH A:651binding site for residue MPD A 505
06AC6SOFTWAREASP A:248 , GLU A:267 , ARG A:268 , TYR A:414 , LYS A:418 , MPD A:513binding site for residue MPD A 506
07AC7SOFTWAREGLY A:140 , TRP A:194 , ASP A:452 , ARG A:453binding site for residue MPD A 507
08AC8SOFTWAREGLU A:127 , LEU A:128 , SER A:159 , PHE A:251 , SER A:334 , HOH A:714binding site for residue MPD A 508
09AC9SOFTWARELEU A:339 , ARG A:436 , HOH A:1087binding site for residue MPD A 509
10AD1SOFTWAREMET A:295 , MET A:355binding site for residue MPD A 510
11AD2SOFTWAREPRO A:28 , GLU A:29 , HOH A:719 , HOH A:952 , HOH A:1016binding site for residue MPD A 511
12AD3SOFTWAREPRO A:144 , PRO A:188 , HIS A:189 , TRP A:194 , HOH A:687binding site for residue MPD A 512
13AD4SOFTWAREVAL A:258 , GLU A:260 , LEU A:261 , PRO A:413 , MPD A:506 , HOH A:900 , HOH A:968binding site for residue MPD A 513
14AD5SOFTWAREPRO A:191 , TRP A:194 , MET A:355 , ARG A:453binding site for residue MPD A 514
15AD6SOFTWARELYS A:104 , THR A:212 , ARG A:280 , LYS A:438 , GLY A:439 , HOH A:737 , HOH A:746binding site for residue MPD A 515
16AD7SOFTWAREGLU A:257 , SER A:259 , ARG A:276 , MPD A:505binding site for residue MPD A 516
17AD8SOFTWAREPRO A:25 , SER A:26 , VAL A:214 , GLN A:216 , ASN A:362 , GLY A:363 , GLN A:364 , HOH A:736 , HOH A:834 , HOH A:878binding site for residue MPD A 517
18AD9SOFTWARELYS A:31 , LEU A:42 , LYS A:43 , GLY A:64 , HOH A:729binding site for residue MPD A 518

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K7A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K7A)

(-) Exons   (0, 0)

(no "Exon" information available for 5K7A)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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.....eeeeeee......eeee......eeee......eeeeeee........................eeeeeeeeee....eeee...........eee....eeeeeeee.....eeeee.....eeeee..ee........eeee....eeeeeee....eeeeeee.hhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k7a 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 5K7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K7A)

(-) Gene Ontology  (5, 5)

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 ]
    MPD  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    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
  5k7a
    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/SwissProt
 
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 5k84
UniProtKB/TrEMBL
        Q72HW2_THET2 | Q72HW2: 2xu9 2xuw 2xvb 2yae 2yaf 2yah 2yam 2yao 2yap 2yaq 2yar 4ai7 5afa

(-) Related Entries Specified in the PDB File

5jrr 5jx9 5k0d 5k15 5k3k 5k5k 5k84