Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 CONSERVED HYPOTHETICAL PROTEIN RV2074 FROM MYCOBACTERIUM TUBERCULOSIS 1.6 A
 
Authors :  B. K. Biswal, K. Au, M. M. Cherney, C. Garen, M. N. James, Tb Structural Consortium (Tbsgc)
Date :  23 Aug 05  (Deposition) - 11 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rv2074, H37Rv, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Biswal, K. Au, M. M. Cherney, C. Garen, M. N. James
The Molecular Structure Of Rv2074, A Probable Pyridoxine 5'-Phosphate Oxidase From Mycobacterium Tuberculosis, At 1. Angstroms Resolution.
Acta Crystallogr. , Sect. F V. 62 735 2006
PubMed-ID: 16880544  |  Reference-DOI: 10.1107/S1744309106025012

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN RV2074
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2MSE1Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECIT A:1001 , CIT A:2001 , HOH A:2057 , HOH A:2113 , HOH A:2128BINDING SITE FOR RESIDUE NA A 1157
2AC2SOFTWARETHR A:55 , THR A:56 , SER A:59 , LYS A:61 , ARG A:112 , ASN A:114 , ARG A:116 , NA A:1157 , CIT A:2001 , HOH A:2005 , HOH A:2021 , HOH A:2062 , HOH A:2113BINDING SITE FOR RESIDUE CIT A 1001
3AC3SOFTWARESER A:59 , GLN A:60 , LYS A:61 , TRP A:81 , PRO A:115 , ARG A:116 , CIT A:1001 , NA A:1157 , HOH A:2008 , HOH A:2053 , HOH A:2081 , HOH A:2100 , HOH A:2113 , HOH A:2122 , HOH A:2144BINDING SITE FOR RESIDUE CIT A 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ASF)

(-) 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:125
 aligned with FBVR_MYCTO | P9WLL6 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:125
                                    20        30        40        50        60        70        80        90       100       110       120       130     
           FBVR_MYCTO    11 SDDALAFLSERHLAMLTTLRADNSPHVVAVGFTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRYRTPRPNPRRVVIEVQIERVLGSADLLD 135
               SCOP domains d2asfa1 A:11-135 Hypothetical protein Rv2074                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....eeeeee.....eeeeee..eee....eeeeeee..hhhhhhhhhhheeeeeeee..eeeeeeeeeeee.hhhhhhhhhhhhhhhh........eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2asf A  11 SDDALAFLSERHLAmLTTLRADNSPHVVAVGFTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRYRTPRPNPRRVVIEVQIERVLGSADLLD 135
                                    20    |   30        40        50        60        70        80        90       100       110       120       130     
                                         25-MSE                                                                                                          


Chain A from PDB  Type:PROTEIN  Length:125
 aligned with FBVR_MYCTU | P9WLL7 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:125
                                    20        30        40        50        60        70        80        90       100       110       120       130     
           FBVR_MYCTU    11 SDDALAFLSERHLAMLTTLRADNSPHVVAVGFTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRYRTPRPNPRRVVIEVQIERVLGSADLLD 135
               SCOP domains d2asfa1 A:11-135 Hypothetical protein Rv2074                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....eeeeee.....eeeeee..eee....eeeeeee..hhhhhhhhhhheeeeeeee..eeeeeeeeeeee.hhhhhhhhhhhhhhhh........eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2asf A  11 SDDALAFLSERHLAmLTTLRADNSPHVVAVGFTFDPKTHIARVITTGGSQKAVNADRSGLAVLSQVDGARWLSLEGRAAVNSDIDAVRDAELRYAQRYRTPRPNPRRVVIEVQIERVLGSADLLD 135
                                    20    |   30        40        50        60        70        80        90       100       110       120       130     
                                         25-MSE
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (FBVR_MYCTU | P9WLL7)
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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
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.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (FBVR_MYCTO | P9WLL6)
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: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:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
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.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.

 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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2asf)
 
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
  2asf
    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
  FBVR_MYCTO | P9WLL6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  FBVR_MYCTU | P9WLL7
    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)
  (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
  FBVR_MYCTO | P9WLL6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  FBVR_MYCTU | P9WLL7
    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
        FBVR_MYCTU | P9WLL7: 5jab

(-) Related Entries Specified in the PDB File

1xxo RELATED ID: RV2074 RELATED DB: TARGETDB