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 :  LIGNIN PEROXIDASE (ISOZYME H2) PI 4.15
 
Authors :  T. H. Choinowski, K. Piontek, T. Glumoff
Date :  09 Nov 95  (Deposition) - 08 Mar 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Heme Protein, Glyco Protein, , Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Choinowski, W. Blodig, K. H. Winterhalter, K. Piontek
The Crystal Structure Of Lignin Peroxidase At 1. 70 A Resolution Reveals A Hydroxy Group On The Cbeta Of Tryptophan 171: A Novel Radical Site Formed During The Redo Cycle.
J. Mol. Biol. V. 286 809 1999
PubMed-ID: 10024453  |  Reference-DOI: 10.1006/JMBI.1998.2507
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIGNIN PEROXIDASE
    Atcc: 24725
    Chains: A
    EC Number: 1.11.1.-
    Organism Scientific: PHANEROCHAETE CHRYSOSPORIUM
    Organism Taxid: 5306
    Strain: BKM-F1267
    Synonym: LIP4.15

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA2Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6OH1Ligand/IonHYDROXIDE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:257 , LYS A:260 , NAG A:361BINDING SITE FOR RESIDUE NAG A 360
2AC2SOFTWARENAG A:360BINDING SITE FOR RESIDUE NAG A 361
3AC3SOFTWARELYS A:7 , GLY A:231 , SER A:334 , VAL A:335 , ALA A:336 , ARG A:337 , HOH A:544 , HOH A:545BINDING SITE FOR RESIDUE MAN A 370
4AC4SOFTWARECYS A:249 , CYS A:317 , GLU A:319 , THR A:320 , HOH A:623 , HOH A:624BINDING SITE FOR RESIDUE A2G A 380
5AC5SOFTWAREASP A:48 , GLY A:66 , ASP A:68 , SER A:70 , HOH A:733 , HOH A:734BINDING SITE FOR RESIDUE CA A 351
6AC6SOFTWARESER A:177 , ASP A:194 , THR A:196 , ILE A:199 , ASP A:201BINDING SITE FOR RESIDUE CA A 352
7AC7SOFTWARETRP A:171 , MET A:172 , ASP A:264 , PHE A:265 , ILE A:268 , HOH A:702BINDING SITE FOR RESIDUE OH A 381
8AC8SOFTWAREHIS A:39 , GLU A:40 , ILE A:42 , ARG A:43 , PHE A:46 , ILE A:85 , GLU A:146 , MET A:172 , LEU A:173 , ALA A:175 , HIS A:176 , ALA A:179 , ALA A:180 , VAL A:181 , ASN A:182 , ASP A:183 , PHE A:193 , ILE A:235 , THR A:237 , HOH A:398 , HOH A:399 , HOH A:562 , HOH A:563 , HOH A:564 , HOH A:565BINDING SITE FOR RESIDUE HEM A 350
9HE3UNKNOWNHEM A:350NULL

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:15
2A:14 -A:285
3A:34 -A:120
4A:249 -A:317

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LLP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LLP)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.LIG2_PHACH66-77  1A:38-49
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.LIG2_PHACH196-206  1A:168-178

(-) Exons   (0, 0)

(no "Exon" information available for 1LLP)

(-) 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:343
 aligned with LIG2_PHACH | P49012 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:343
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368   
           LIG2_PHACH    29 ATCANGKTVGDASCCAWFDVLDDIQANMFHGGQCGAEAHESIRLVFHDSIAISPAMEAKGKFGGGGADGSIMIFDTIETAFHPNIGLDEVVAMQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRKPATQPAPDGLVPEPFHTVDQIIARVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQFRGTLFPGSGGNQGEVESGMAGEIRIQTDHTLARDSRTACEWQSFVGNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPLSKPIPGNGPFSFFPPGKSHSDIEQACAETPFPSLVTLPGPATSVARIPPHKA 371
               SCOP domains d1llpa_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------1llpA01 A:11-144,A:269-299  [code=1.10.520.10, no name defined]                                                                       1llpA02 A:145-268,A:300-339 Peroxidase, domain 2                                                                            1llpA01 A:11-144,A:269-299     1llpA02 A:145-268,A:300-339             ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhh...........hhhh.hhhh...hhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........ee....................hhhhhhhhhhhh...hhhhhhhhhhhhh.ee.........ee..........hhhhh................ee........eehhhhhh................hhhhhhhhhhhhhhhh.....hhh.ee.hhh.....................hhh............................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1llp A   1 ATCANGKTVGDASCCAWFDVLDDIQANMFHGGQCGAEAHESIRLVFHDSIAISPAMEAKGKFGGGGADGSIMIFDTIETAFHPNIGLDEVVAMQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRKPATQPAPDGLVPEPFHTVDQIIARVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQFRGTLFPGSGGNQGEVESGMAGEIRIQTDHTLARDSRTACEWQSFVGNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPLSKPIPGNGPFSFFPPGKSHSDIEQACAETPFPSLVTLPGPATSVARIPPHKA 343
                                    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
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LLP)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIG2_PHACH | P49012)
molecular function
    GO:0016690    diarylpropane peroxidase activity    Catalysis of the reaction: (3,4-dimethoxyphenyl)methanol + H2O2 = 3,4-dimethoxybenzaldehyde + 2 H2O.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0046274    lignin catabolic process    The chemical reactions and pathways resulting in the breakdown of lignins, a class of polymers of phenylpropanoid units.
    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.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

 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
    A2G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
    HE3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1llp)
 

(-) 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
  1llp
    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
  LIG2_PHACH | P49012
    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)
  1.11.1.-
    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
  LIG2_PHACH | P49012
    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
        LIG2_PHACH | P49012: 1lga

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LLP)