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 :  CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION. (DR_2006) FROM DEINOCOCCUS RADIODURANS AT 1.88 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Jun 10  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein With Unknown Function, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Protein With Unknown Function. (Dr_2006) From Deinococcus Radiodurans At 1. 88 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DR_2006
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:62 , HOH A:194 , HOH A:214 , HOH A:302 , ASP B:62 , HOH B:190BINDING SITE FOR RESIDUE CA A 158
2AC2SOFTWAREVAL A:24 , ALA A:30 , GLY A:94BINDING SITE FOR RESIDUE MRD A 161
3AC3SOFTWAREGLN A:95 , ALA A:105 , HOH A:180 , HOH A:261BINDING SITE FOR RESIDUE MRD A 163
4AC4SOFTWAREHOH A:264 , MSE B:1 , SER B:4 , GLU B:140 , HOH B:184 , HOH B:202 , HOH B:353BINDING SITE FOR RESIDUE CA B 159
5AC5SOFTWAREGLU B:6 , HOH B:176 , HOH B:234 , HOH B:333 , HOH B:337BINDING SITE FOR RESIDUE CA B 160
6AC6SOFTWAREVAL B:24 , PRO B:27 , LEU B:31 , ALA B:76 , LEU B:78 , GLY B:94 , GLN B:95BINDING SITE FOR RESIDUE MRD B 162

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NQN)

(-) 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:151
 aligned with Q9RSW5_DEIRA | Q9RSW5 from UniProtKB/TrEMBL  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
         Q9RSW5_DEIRA     3 LSAEQSFTLRHPHGQAAALAFVREPAAALAGVRFLRGLDSDGEQVWGELLVTVPLLGEVDLPFRSEIVRTPQGAELRPLTLTGERAWVAVSGQATAAEGGEMAFAFQFQAHLATPEAEGWGGAAFEKMVQAAAGRTLERVAKALPEGLAAGLPPA 157
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhhhhhhhhh......eeeee...eeeeeeeeee...eeeeeeeeeeeeee..eeeeee........eeeeeeeeee....eeeeeeeeeee..----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nqn A   3 LSAEQSFTLRHPHGQAAALAFVREPAAALAGVRFLRGLDSDGEQVWGELLVTVPLLGEVDLPFRSEIVRTPQGAELRPLTLTGERAWVAVSGQATAAEGGEmAFAFQFQAHLA----EGWGGAAFEKmVQAAAGRTLERVAKALPEGLAAGLPPA 157
                                    12        22        32        42        52        62        72        82        92       102 |     112  |    122       132       142       152     
                                                                                                                               104-MSE    115  120       130-MSE                       


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q9RSW5_DEIRA | Q9RSW5 from UniProtKB/TrEMBL  Length:157

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
         Q9RSW5_DEIRA     - -MILSAEQSFTLRHPHGQAAALAFVREPAAALAGVRFLRGLDSDGEQVWGELLVTVPLLGEVDLPFRSEIVRTPQGAELRPLTLTGERAWVAVSGQATAAEGGEMAFAFQFQAHLATPEAEGWGGAAFEKMVQAAAGRTLERVAKALPEGLAAGLPP 156
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------DUF3809-3nqnB01 B:8-146                                                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) --------DUF3809-3nqnB02 B:8-146                                                                                                                    ---------- Pfam domains (2)
         Sec.struct. author ....eeeeeeeee...hhhhhhhhhhhhhhhhhh....eeeee...eeeeeeeeee...eeeeeeeeeeeeee..eeeeee........eeeeeeeeee....eeeeeeeeeee...-------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nqn B   0 GmILSAEQSFTLRHPHGQAAALAFVREPAAALAGVRFLRGLDSDGEQVWGELLVTVPLLGEVDLPFRSEIVRTPQGAELRPLTLTGERAWVAVSGQATAAEGGEmAFAFQFQAHLAT-------GAAFEKmVQAAAGRTLERVAKALPEGLAAGLPP 156
                             |       9        19        29        39        49        59        69        79        89        99    |  109      |  -    |  129|      139       149       
                             1-MSE                                                                                                104-MSE     116     124     |                          
                                                                                                                                                            130-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 3NQN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF3809] (1)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9RSW5_DEIRA | Q9RSW5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nqn)
 

(-) 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
  3nqn
    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
  Q9RSW5_DEIRA | Q9RSW5
    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
  Q9RSW5_DEIRA | Q9RSW5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9RSW5_DEIRA | Q9RSW5: 5im6

(-) Related Entries Specified in the PDB File

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