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 :  THE FLAVOPROTEIN NRDI FROM BACILLUS CEREUS WITH THE INITIALLY SEMIQUINONE FMN COFACTOR IN AN INTERMEDIATE RADIATION REDUCED STATE
 
Authors :  A. K. Rohr, H. P. Hersleth, K. K. Andersson
Date :  15 Jan 10  (Deposition) - 09 Mar 10  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribonucleotide Reductase, Flavodoxin, Electron Transfer, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Rohr, H. P. Hersleth, K. K. Andersson
Tracking Flavin Conformations In Protein Crystal Structures With Raman Spectroscopy And Qm/Mm Calculations
Angew. Chem. Int. Ed. Engl. V. 49 2324 2010
PubMed-ID: 20187055  |  Reference-DOI: 10.1002/ANIE.200907143

(-) Compounds

Molecule 1 - NRDI PROTEIN
    Atcc: 14579
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Synonym: NRDI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:7 , MET A:8 , THR A:9 , GLY A:10 , ASN A:11 , VAL A:12 , ASN A:20 , TYR A:41 , THR A:42 , GLY A:44 , GLY A:46 , SER A:69 , GLY A:70 , ASN A:71 , TRP A:74 , MET A:77 , PHE A:78 , GLY A:79 , LEU A:99 , HOH A:2055 , HOH A:2127 , HOH A:2128BINDING SITE FOR RESIDUE FMN A1119
2AC2SOFTWAREHIS A:17 , GLU A:98 , CAC A:1124 , HOH A:2129BINDING SITE FOR RESIDUE ZN A1120
3AC3SOFTWAREGLU A:50 , ASP A:54 , GLU A:111 , ZN A:1123 , HOH A:2130 , HOH A:2133BINDING SITE FOR RESIDUE ZN A1121
4AC4SOFTWAREGLU A:57 , ASP A:76 , ZN A:1123BINDING SITE FOR RESIDUE ZN A1122
5AC5SOFTWAREGLU A:50 , ASP A:54 , ZN A:1121 , ZN A:1122 , HOH A:2133 , HOH A:2134 , HOH A:2135 , HOH A:2136BINDING SITE FOR RESIDUE ZN A1123
6AC6SOFTWARETYR A:5 , HIS A:17 , GLU A:98 , ZN A:1120 , HOH A:2016 , HOH A:2137BINDING SITE FOR RESIDUE CAC A1124

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X2P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X2P)

(-) Exons   (0, 0)

(no "Exon" information available for 2X2P)

(-) 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:117
 aligned with Q81G57_BACCR | Q81G57 from UniProtKB/TrEMBL  Length:119

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
         Q81G57_BACCR     1 MLVAYDSMTGNVKRFIHKLNMPAVQIDEDLVIDEDFILITYTTGFGNVPERVLDFLERNNEKLKGVSASGNRNWGDMFGASADKISTKYEVPIVSKFELSGTNNDVEYFKERVREIA 117
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x2pA00 A:1-117  [code=3.40.50.360, no name defined]                                                                  CATH domains
               Pfam domains --Flavodoxin_NdrI-2x2pA01 A:3-111                                                                              ------ Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhh..eee..........eeeeee.......hhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2x2p A   1 MLVAYDSMTGNVKRFIHKLNMPAVQIDEDLVIDEDFILITYTTGFGNVPERVLDFLERNNEKLKGVSASGNRNWGDMFGASADKISTKYEVPIVSKFELSGTNNDVEYFKERVREIA 117
                                    10        20        30        40        50        60        70        80        90       100       110
   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 2X2P)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q81G57_BACCR | Q81G57)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

 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
    CAC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x2p)
 

(-) 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
  2x2p
    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
  Q81G57_BACCR | Q81G57
    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
  Q81G57_BACCR | Q81G57
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q81G57_BACCR | Q81G57: 2x2o 4bmp

(-) Related Entries Specified in the PDB File

2x2o THE FLAVOPROTEIN NRDI FROM BACILLUS CEREUS WITH THE INITIALLY OXIDIZED FMN COFACTOR IN AN INTERMEDIATE RADIATION REDUCED STATE