Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN DR1152 FROM DEINOCOCCUS RADIODURANS R1, PFAM DUF861
 
Authors :  A. A. Fedorov, E. V. Fedorov, S. C. Almo, S. K. Burley, New York Sgx Res Center For Structural Genomics (Nysgxrc)
Date :  20 Feb 04  (Deposition) - 22 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Biol. Unit 3:  A  (4x)
Biol. Unit 4:  B  (4x)
Keywords :  Structural Genomics, Nysgxrc Target T1583, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, S. C. Almo
Crystal Structure Of Conserved Hypothetical Protein From Deinicoccus Radiodurans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): AB
Biological Unit 3 (4x): A 
Biological Unit 4 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1SFN)

(-) Sites  (0, 0)

(no "Site" information available for 1SFN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SFN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SFN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SFN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SFN)

(-) Exons   (0, 0)

(no "Exon" information available for 1SFN)

(-) 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:245
 aligned with Q9RV77_DEIRA | Q9RV77 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
        Q9RV77_DEIRA      1 MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHIAPVVGLGARFVQFTAEMPAGAQATESVYQRFAFVLSGEVDVAVGGETRTLREYDYVYLPAGEKHMLTAKTDARVSVFEKPYQTVEGVQAPGVYWGNERENPGYPFEGDDHLIARKLLPDEPAFDFMVSTMSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDIIWMGAHCPQWYGALGRNWSKYLLYKDMNRHPL  245
               SCOP domains d1sfna_ A: Hypothetical protein DR1152                                                                                                                                                                                                                SCOP domains
               CATH domains 1sfnA00 A:1001-1245 Jelly Rolls                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....eee..eeeehhhhh...........eeeeee..........eeeeeee....eee....eeeeeeeeeeeeee....eeee...eeeee......eeeeeeeeeeeeeee.............eeee......ee......eeeee.........eeeeeeee...............eeeeeee.eeeeee..eeeeee...eeee.....eeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sfn A 1001 MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHIAPVVGLGARFVQFTAEMPAGAQATESVYQRFAFVLSGEVDVAVGGETRTLREYDYVYLPAGEKHMLTAKTDARVSVFEKPYQTVEGVQAPGVYWGNERENPGYPFEGDDHLIARKLLPDEPAFDFMVSTMSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDIIWMGAHCPQWYGALGRNWSKYLLYKDMNRHPL 1245
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240     


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q9RV77_DEIRA | Q9RV77 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
        Q9RV77_DEIRA      1 MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHIAPVVGLGARFVQFTAEMPAGAQATESVYQRFAFVLSGEVDVAVGGETRTLREYDYVYLPAGEKHMLTAKTDARVSVFEKPYQTVEGVQAPGVYWGNERENPGYPFEGDDHLIARKLLPDEPAFDFMVSTMSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDIIWMGAHCPQWYGALGRNWSKYLLYKDMNRHPL  245
               SCOP domains d1sfnb_ B: Hypothetical protein DR1152                                                                                                                                                                                                                SCOP domains
               CATH domains 1sfnB00 B:2001-2245 Jelly Rolls                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -------------------------------------------Cupin_3-1sfnB03 B:2044-2121                                                   ----------------------------------------------Cupin_2-1sfnB01 B:2168-2236                                          --------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------Cupin_3-1sfnB04 B:2044-2121                                                   ----------------------------------------------Cupin_2-1sfnB02 B:2168-2236                                          --------- Pfam domains (2)
         Sec.struct. author hhhhh....ee...eeeehhhhh...........eeeeee..........eeeeeee....eee....eeeeeeee..eeeee..eeeee...eeeee.....eeeee...eeeeeeee.............eeee......ee......eeeee.........eeeeeeee...............eeeeeee.eeeeee..eeeeee...eeee.....eeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sfn B 2001 MKHLGQTRSALHGSHAVITPETFVRTALAEWPGSAIVLHIAPVVGLGARFVQFTAEMPAGAQATESVYQRFAFVLSGEVDVAVGGETRTLREYDYVYLPAGEKHMLTAKTDARVSVFEKPYQTVEGVQAPGVYWGNERENPGYPFEGDDHLIARKLLPDEPAFDFMVSTMSFAPGASLPYAEVHYMEHGLLMLEGEGLYKLEENYYPVTAGDIIWMGAHCPQWYGALGRNWSKYLLYKDMNRHPL 2245
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1SFN)

 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
(no "Ligands, Modified Residues, Ions" information available for 1sfn)
 
  Sites
(no "Sites" information available for 1sfn)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sfn)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  1sfn
    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
  Q9RV77_DEIRA | Q9RV77
    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
  Q9RV77_DEIRA | Q9RV77
    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 1SFN)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SFN)