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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE Q5LES9_BACFN PROTEIN FROM BACTEROIDES FRAGILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BFR250.
 
Authors :  S. Vorobiev, H. Neely, J. Seetharaman, D. Wang, C. Ciccosanti, E. L. Foote, S. Sahdev, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  06 Nov 09  (Deposition) - 24 Nov 09  (Release) - 24 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Putative Methyltransferase, Bfr250, Nesg, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vorobiev, H. Neely, J. Seetharaman, D. Wang, C. Ciccosanti, E. L. Foote, S. Sahdev, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Q5Les9_bacfn Protein From Bacteroides Fragilis.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN Q5LES9
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 21-23C
    Expression System Strain: BL21(DE3) +MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BF1671
    Organism Scientific: BACTEROIDES FRAGILIS NCTC 9343
    Organism Taxid: 272559
    Strain: ATCC 25285/NCTC 9343

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , GLN A:26 , GLY A:27 , GLY A:54 , CYS A:55 , GLY A:56 , GLN A:60 , ASP A:76 , PHE A:77 , PHE A:81 , GLY A:103 , SER A:104 , MSE A:105 , GLU A:121 , GLY A:122 , ASN A:126 , HOH A:404 , HOH A:421BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWAREARG B:25 , GLN B:26 , GLY B:27 , GLY B:54 , CYS B:55 , GLY B:56 , GLN B:60 , ASP B:76 , PHE B:77 , PHE B:81 , GLY B:103 , SER B:104 , MSE B:105 , GLU B:121 , GLY B:122 , ASN B:126 , HOH B:409 , HOH B:442 , HOH B:447BINDING SITE FOR RESIDUE SAM B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KKZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KKZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KKZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KKZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3KKZ)

(-) 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:256
 aligned with Q5LES9_BACFN | Q5LES9 from UniProtKB/TrEMBL  Length:259

    Alignment length:256
                                                                                                                                                                                                                                                                                       259  
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   |  
         Q5LES9_BACFN     6 KTIHDFELNLICDFFSNMERQGPGSPEVTLKALSFIDNLTEKSLIADIGCGTGGQTMVLAGHVTGQVTGLDFLSGFIDIFNRNARQSGLQNRVTGIVGSMDDLPFRNEELDLIWSEGAIYNIGFERGLNEWRKYLKKGGYLAVSECSWFTDERPAEINDFWMDAYPEIDTIPNQVAKIHKAGYLPVATFILPENCWTDHYFTPKVAAQKIFLTKYAGNKIAEEFSMLQSIEEELYHKYKEYYGYTFFIAKKIRL--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhh.........eeeee....hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.....eeeee............eeeeee..hhhhhhhhhhhhhhh..eeeeeeeeeeeeee.....hhhhhhhhhhhh...eehhhhhhhhhhh.eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kkz A   6 KTIHDFELNLICDFFSNmERQGPGSPEVTLKALSFIDNLTEKSLIADIGCGTGGQTmVLAGHVTGQVTGLDFLSGFIDIFNRNARQSGLQNRVTGIVGSmDDLPFRNEELDLIWSEGAIYNIGFERGLNEWRKYLKKGGYLAVSECSWFTDERPAEINDFWmDAYPEIDTIPNQVAKIHKAGYLPVATFILPENCWTDHYFTPKVAAQKIFLTKYAGNKIAEEFSmLQSIEEELYHKYKEYYGYTFFIAKKIRLLE 261
                                    15       |25        35        45        55      | 65        75        85        95       105       115       125       135       145       155       165 |     175       185       195       205       215       225     | 235       245       255      
                                            23-MSE                                 62-MSE                                    105-MSE                                                       167-MSE                                                         231-MSE                          


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with Q5LES9_BACFN | Q5LES9 from UniProtKB/TrEMBL  Length:259

    Alignment length:250
                                                                                                                                                                                                                                                                                 259  
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       | -
         Q5LES9_BACFN    12 ELNLICDFFSNMERQGPGSPEVTLKALSFIDNLTEKSLIADIGCGTGGQTMVLAGHVTGQVTGLDFLSGFIDIFNRNARQSGLQNRVTGIVGSMDDLPFRNEELDLIWSEGAIYNIGFERGLNEWRKYLKKGGYLAVSECSWFTDERPAEINDFWMDAYPEIDTIPNQVAKIHKAGYLPVATFILPENCWTDHYFTPKVAAQKIFLTKYAGNKIAEEFSMLQSIEEELYHKYKEYYGYTFFIAKKIRL--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------Methyltransf_31-3kkzB01 B:44-241                                                                                                                                                                      -------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------Methyltransf_31-3kkzB02 B:44-241                                                                                                                                                                      -------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh........hhhhhhhhhh.........eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee............eeeeee..hhhhhhhhhhhhhhh..eeeeeeeeeeeeee.....hhhhhhhhhhhh...eehhhhhhhhhhh.eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kkz B  12 ELNLICDFFSNmERQGPGSPEVTLKALSFIDNLTEKSLIADIGCGTGGQTmVLAGHVTGQVTGLDFLSGFIDIFNRNARQSGLQNRVTGIVGSmDDLPFRNEELDLIWSEGAIYNIGFERGLNEWRKYLKKGGYLAVSECSWFTDERPAEINDFWmDAYPEIDTIPNQVAKIHKAGYLPVATFILPENCWTDHYFTPKVAAQKIFLTKYAGNKIAEEFSmLQSIEEELYHKYKEYYGYTFFIAKKIRLLE 261
                                    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
                                      23-MSE                                 62-MSE                                    105-MSE                                                       167-MSE                                                         231-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 3KKZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KKZ)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5LES9_BACFN | Q5LES9)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kkz)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  3kkz
    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
  Q5LES9_BACFN | Q5LES9
    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
  Q5LES9_BACFN | Q5LES9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3KKZ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KKZ)