Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 BACILLUS SUBTILIS YVQK, A PUTATIVE ATP-BINDING COBALAMIN ADENOSYLTRANSFERASE, THE NORTH EAST STRUCTURAL GENOMICS TARGET SR128
 
Authors :  F. Forouhar, I. Lee, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  10 Dec 03  (Deposition) - 23 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  All Alpha-Helical Trimeric Protein, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, A. Kuzin, J. Seetharaman, I. Lee, W. Zhou, M. Abashidze, Y. Chen, W. Yong, H. Janjua, Y. Fang, D. Wang, K. Cunningham, R. Xiao, T. B. Acton, E. Pichersky, D. F. Klessig, C. W. Porter, G. T. Montelione, L. Tong
Functional Insights From Structural Genomics.
J. Struct. Funct. Genom. V. 8 37 2007
PubMed-ID: 17588214  |  Reference-DOI: 10.1007/S10969-007-9018-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YVQK PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YVQK
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:131 , ARG A:135 , ARG B:131 , ARG B:135 , ARG C:131 , ARG C:135 , HOH C:196 , HOH A:197 , HOH A:232BINDING SITE FOR RESIDUE PO4 A 194

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RTY)

(-) 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:158
 aligned with PDUO_BACSU | O34899 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:161
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
           PDUO_BACSU    22 KDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVTERKDYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALMKSEEIHETVLRYLNRLSDYFFAAARVVNARSGIGDVEYERSA 182
               SCOP domains d1rtya_ A: Putative ATP-binding cobalamin adenosyltransfe   rase YvqK                                                                                             SCOP domains
               CATH domains 1rtyA00 A:22-182  [code=1.20.1200.10, no name defined]                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..---....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rty A  22 KDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVT---DYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALmKSEEIHETVLRYLNRLSDYFFAGARVVNARSGIGDVEYERSA 182
                                    31        41        51        61        71      |  -|       91       101       111       121       131       141       151       161       171       181 
                                                                                   78  82                                                       140-MSE                                      


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with PDUO_BACSU | O34899 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           PDUO_BACSU     1 MKLYTKTGDKGQTGLVGGRTDKDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVTERKDYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALMKSEEIHETVLRYLNRLSDYFFAAARVVNARSGIGDVEYER 180
               SCOP domains d1rty                 b_ B: Putative ATP-binding cobalamin adenosyltransferase YvqK                                                                                                  SCOP domains
               CATH domains -1rty                 B00 B:2-180  [code=1.20.1200.10, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rty B   1 mKLYT-----------------DSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVTERKDYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALmKSEEIHETVLRYLNRLSDYFFAGARVVNARSGIGDVEYER 180
                            |   |    -         -  |     30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
                            1-MSE                23                                                                                                                  140-MSE                                    


Chain C from PDB  Type:PROTEIN  Length:162
 aligned with PDUO_BACSU | O34899 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:169
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
           PDUO_BACSU    22 KDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVTERKDYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALMKSEEIHETVLRYLNRLSDYFFAAARVVNARSGIGDVEYERSAIVFRDRNS 190
               SCOP domains d1rtyc_ C: Putative ATP-binding cobalamin adenosyltran       sferase YvqK                                                                                                 SCOP domains
               CATH domains 1rtyC00 C:22-190  [code=1.20.1200.10, no name defined]                                                                                                                    CATH domains
           Pfam domains (1) Cob_adeno_trans-1rtyC01 C:22-168                                                                                                                   ---------------------- Pfam domains (1)
           Pfam domains (2) Cob_adeno_trans-1rtyC02 C:22-168                                                                                                                   ---------------------- Pfam domains (2)
           Pfam domains (3) Cob_adeno_trans-1rtyC03 C:22-168                                                                                                                   ---------------------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh-------...hhhhhhhhhhhhhhhhhhh......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rty C  22 KDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLA-------YKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALmKSEEIHETVLRYLNRLSDYFFAGARVVNARSGIGDVEYERSAIVFRDRNS 190
                                    31        41        51        61        71   |     - |      91       101       111       121       131       141       151       161       171       181         
                                                                                75      83                                                      140-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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Cob_adeno_trans] (11)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PDUO_BACSU | O34899)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008817    cob(I)yrinic acid a,c-diamide adenosyltransferase activity    Catalysis of the reaction: ATP + cob(I)alamin + H2O = phosphate + diphosphate + adenosylcobalamin.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009236    cobalamin biosynthetic process    The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rty)
 

(-) 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
  1rty
    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
  PDUO_BACSU | O34899
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  PDUO_BACSU | O34899
    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 1RTY)

(-) Related Entries Specified in the PDB File

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