Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE COMPLEXED WITH NADP(H)
 
Authors :  Y. Kim, H. J. Park, S. N. Kwak, J. S. Lee, T. K. Oh, M. H. Kim
Date :  31 Mar 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Reductase, Sdr Family, Oxidoreductase, Triphenylmethane Reduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Kim, Y. Kim, H. J. Park, J. S. Lee, S. N. Kwak, W. H. Jung, S. G. Lee, D. Kim, Y. C. Lee, T. K. Oh
Structural Insight Into Bioremediation Of Triphenylmethane Dyes By Citrobacter Sp. Triphenylmethane Reductase.
J. Biol. Chem. V. 283 31981 2008
PubMed-ID: 18782772  |  Reference-DOI: 10.1074/JBC.M804092200

(-) Compounds

Molecule 1 - TRIPHENYLMETHANE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSSETA GAMI (DE3)
    Expression System Taxid: 562
    Organism Scientific: CITROBACTER SP. MY-5
    Organism Taxid: 308866

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , THR A:9 , GLY A:10 , GLN A:11 , LEU A:12 , ARG A:34 , GLY A:52 , ASP A:53 , TYR A:54 , ASN A:55 , ILE A:73 , SER A:74 , GLY A:75 , PRO A:76 , ALA A:141 , LEU A:142 , TYR A:143 , ARG A:175 , HOH A:2001 , HOH A:2002 , HOH A:2008 , HOH A:2134 , HOH A:2135 , HOH A:2136BINDING SITE FOR RESIDUE NAP A1286

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VRB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VRB)

(-) Sequences/Alignments

Asymmetric 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:284
 aligned with Q2TNI4_9ENTR | Q2TNI4 from UniProtKB/TrEMBL  Length:287

    Alignment length:284
                                    11        21        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    
         Q2TNI4_9ENTR     2 SIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASIESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -NmrA-2vrbA01 A:3-227                                                                                                                                                                                                             ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeee....hhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh..hhhhhhhhhhhhhhhhh..eeeeee...hhhh...hhhhhhhhheeee.....ee...hhhhhhhhhhhhhh......eeeee.....eehhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrb A   2 SIAVTGATGQLGGLVIQHLLKKVPASQIIAIVRNVEKASTLADQGVEVRHGDYNQPESLQKAFAGVSKLLFISGPHYDNTLLIVQHANVVKAARDAGVKHIAYTGYAFAEESIIPLAHVHLATEYAIRTTNIPYTFLRNALYTDFFVNEGLRASTESGAIVTNAGSGIVNSVTRNELALAAATVLTEEGHENKTYNLVSNQPWTFDELAQILSEVSGKKVVHQPVSFEEEKNFLVNAGVPEPFAEITAAIYDAISKGEASKTSDDLQKLIGSLTPLKETVKQAL 285
                                    11        21        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
   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 2VRB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q2TNI4_9ENTR | Q2TNI4)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 Visualization

(-) Interactive Views

Asymmetric 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
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vrb)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2vrb
    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
  Q2TNI4_9ENTR | Q2TNI4
    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
  Q2TNI4_9ENTR | Q2TNI4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q2TNI4_9ENTR | Q2TNI4: 2jl1 2vrc

(-) Related Entries Specified in the PDB File

2jl1 STRUCTURAL INSIGHT INTO BIOREMEDIATION OF TRIPHENYLMETHANE DYES BY CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE
2vrc CRYSTAL STRUCTURE OF THE CITROBACTER SP. TRIPHENYLMETHANE REDUCTASE COMPLEXED WITH NADP(H)