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

(-) Description

Title :  CRYSTAL STRUCTURE OF GENOMICS APC5600
 
Authors :  A. Dong, T. Skarina, A. Savchenko, E. F. Pai, A. Joachimiak, A. Edwards, Center For Structural Genomics (Mcsg)
Date :  24 Jan 05  (Deposition) - 08 Mar 05  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Sulfur Sad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dong, T. Skarina, A. Savchenko, E. F. Pai, A. Edwards
Crystal Structure Of Genomics Af1432 By Sulfur Sad Methods
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AF1432
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AF1432
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1YNB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YNB)

(-) 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:167
 aligned with O28840_ARCFU | O28840 from UniProtKB/TrEMBL  Length:173

    Alignment length:167
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       
         O28840_ARCFU     7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHSFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWWR 173
               SCOP domains d1ynba1 A:7-173 Hypothetical protein AF1432                                                                                                                             SCOP domains
               CATH domains 1ynbA00 A:7-173 Hypothetical protein af1432                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhh....hhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ynb A   7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHNFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWWR 173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with O28840_ARCFU | O28840 from UniProtKB/TrEMBL  Length:173

    Alignment length:167
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       
         O28840_ARCFU     7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHSFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWWR 173
               SCOP domains d1ynbb_ B: Hypothetical protein AF1432                                                                                                                                  SCOP domains
               CATH domains 1ynbB00 B:7-173 Hypothetical protein af1432                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhh....hhhh.eeehhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ynb B   7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHNFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWWR 173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       


Chain C from PDB  Type:PROTEIN  Length:167
 aligned with O28840_ARCFU | O28840 from UniProtKB/TrEMBL  Length:173

    Alignment length:167
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       
         O28840_ARCFU     7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHSFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWWR 173
               SCOP domains d1ynbc_ C: Hypothetical protein AF1432                                                                                                                                  SCOP domains
               CATH domains 1ynbC00 C:7-173 Hypothetical protein af1432                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhh..hhhhhh.eeehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ynb C   7 MDDVVKFIHEVGSLKLTPRSGWLKLGIRLPESVAEHNFRAAIIAFILALKSGESVEKACKAATAALFHDLHEARTMDLHKIARRYVSCDEEGAREEQLSWMESKPDFSDVEVYVSDADKLELAFQGVEYSQQVSYAIRFAENVELKTDAAKEIYRVLMERKNPVWWR 173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166
   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, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YNB)

(-) Gene Ontology  (0, 0)

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

 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 1ynb)
 
  Sites
(no "Sites" information available for 1ynb)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ynb)
 
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 | Biol. Unit 1 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
  1ynb
    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
  O28840_ARCFU | O28840
    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
  O28840_ARCFU | O28840
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O28840_ARCFU | O28840: 1yoy

(-) Related Entries Specified in the PDB File

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