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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STREPTOCOCCUS PNEUMONIA TIGR4 FLAVODOXIN: STRUCTURAL AND BIOPHYSICAL CHARACTERIZATION OF A NOVEL DRUG TARGET
 
Authors :  A. Rodriguez-Cardenas, A. L. Rojas, A. Velazquez-Campoy, R. Hurtado- J. Sancho
Date :  18 Jul 16  (Deposition) - 31 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Flavodoxin, Protein Stability, Fmn Binding, Drug Target, Streptococcus Pneumoniae, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rodriguez-Cardenas, A. L. Rojas, M. Conde-Gimenez, A. Velazquez-Campoy, R. Hurtado-Guerrero, J. Sancho
Streptococcus Pneumoniae Tigr4 Flavodoxin: Structural And Biophysical Characterization Of A Novel Drug Target.
Plos One V. 11 61020 2016
PubMed-ID: 27649488  |  Reference-DOI: 10.1371/JOURNAL.PONE.0161020

(-) Compounds

Molecule 1 - FLAVODOXIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: AWW74_08705
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:10 , MSE A:11 , THR A:12 , GLY A:13 , ASN A:14 , THR A:15 , TYR A:57 , THR A:58 , TYR A:59 , GLY A:60 , SER A:90 , GLY A:91 , ASP A:92 , TYR A:95 , GLU A:97 , PHE A:98 , CYS A:99 , LEU A:125 , HOH A:309binding site for residue FMN A 201
2AC2SOFTWAREASP A:34 , ASP A:36 , ASP C:36 , CA C:202 , HOH C:309binding site for residue CA A 202
3AC3SOFTWAREASP A:77 , ASP C:61 , GLU C:63 , CA C:206 , HOH C:322 , HOH C:330binding site for residue CA A 203
4AC4SOFTWARESER C:10 , MSE C:11 , THR C:12 , GLY C:13 , ASN C:14 , THR C:15 , TYR C:57 , THR C:58 , TYR C:59 , GLY C:60 , SER C:90 , GLY C:91 , ASP C:92 , TYR C:95 , GLU C:97 , PHE C:98 , CYS C:99 , LEU C:125 , HOH C:308binding site for residue FMN C 201
5AC5SOFTWAREASP A:36 , CA A:202 , HOH A:310 , HOH A:324 , ASP C:34 , ASP C:36binding site for residue CA C 202
6AC6SOFTWAREASP C:28 , ASP C:124 , SER C:126 , HOH C:306 , HOH C:333binding site for residue CA C 203
7AC7SOFTWAREASP A:61 , ASP C:61 , ASP C:77 , HOH C:313 , HOH C:320 , HOH C:331binding site for residue CA C 204
8AC8SOFTWAREASP A:61 , ASP A:77 , HOH A:308 , HOH A:319 , HOH A:328 , HOH A:332 , ASP C:61binding site for residue CA C 205
9AC9SOFTWAREASP A:77 , CA A:203 , ASP C:61 , GLU C:63 , HOH C:322 , HOH C:330binding site for residue CA C 206

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu C:129 -Glu C:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LJI)

(-) 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:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhh..ee....eeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lji A   2 ALAKIVFASmTGNTEEIADIVADKLRDLGLDVDVDECTTVDASDFLEADIAIVATYTYGDGELPDEmmDFYEDLADLNLNGKIYGVVGSGDTFYDEFCKAVDDFDRVFVSTGAEKGSECVKVDLSAEEEDIERLEQFAEELAAKV 146
                                    11        21        31        41        51        61      ||71        81        91       101       111       121       131       141     
                                    11-MSE                                                   68-MSE                                                                          
                                                                                              69-MSE                                                                         


Chain C from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhh..ee....eeee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lji C   2 ALAKIVFASmTGNTEEIADIVADKLRDLGLDVDVDECTTVDASDFLEADIAIVATYTYGDGELPDEmmDFYEDLADLNLNGKIYGVVGSGDTFYDEFCKAVDDFDRVFVSTGAEKGSECVKVDLSAEEEDIERLEQFAEELAAKV 146
                                    11        21        31        41        51        61      ||71        81        91       101       111       121       131       141     
                                    11-MSE                                                   68-MSE                                                                          
                                                                                              69-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  (0, 0)

(no "SCOP Domain" information available for 5LJI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Glu C:129 - Glu C:130   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  5lji
    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
  A0A0B7M5W3_S | A0A0B7M5W3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q8DPG4_STRR6 | Q8DPG4
    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
  A0A0B7M5W3_S | A0A0B7M5W3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q8DPG4_STRR6 | Q8DPG4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8DPG4_STRR6 | Q8DPG4: 5ljl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LJI)