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 YDCK FROM SALMONELLA CHOLERAE AT 2.38 A RESOLUTION. NORTHEAST STRUCTURAL GENOMICS TARGET SCR6
 
Authors :  J. Benach, Y. Chen, S. M. Vorobiev, J. Seetharaman, C. K. Ho, H. Janjua, K. Conover, L-C. Ma, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  13 Apr 07  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Scr6, Nesg, Ydck, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Benach, Y. Chen, S. M. Vorobiev, J. Seetharaman, C. K. Ho, H. Janjua, K. Conover, L-C. Ma, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of Ydck From Salmonella Cholerae At 2. 38 A Resolution.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE TRANSFERASE
    Atcc: 9150
    Chains: A, B
    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: YDCK, SPA1259
    Organism Scientific: SALMONELLA PARATYPHI
    Organism Taxid: 54388
    Strain: SARB42

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:183 , CYS A:205BINDING SITE FOR RESIDUE ZN A 335
2AC2SOFTWARETHR A:220 , GLU A:241BINDING SITE FOR RESIDUE ZN A 336
3AC3SOFTWARETHR B:220 , GLU B:241BINDING SITE FOR RESIDUE ZN B 335

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PIG)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:261 -Pro A:262
2Gly A:307 -Pro A:308
3Gly B:261 -Pro B:262
4Gly B:307 -Pro B:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PIG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PIG)

(-) Exons   (0, 0)

(no "Exon" information available for 2PIG)

(-) 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:310
 aligned with A0A0H2WQ05_S | A0A0H2WQ05 from UniProtKB/TrEMBL  Length:326

    Alignment length:318
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        
         A0A0H2WQ05_S     3 KYRLSEGPRAFTYQVDGEKKSVLLRQVIAVTDFNDVKAGTSGGWVDADNVLSQQGDCWIYDENAMAFAGTEITGNARITQPCTLYNNVRIGDNVWIDRADISDGARISDNVTIQSSSVREECAIYGDARVLNQSEILAIQGLTHEHAQILQIYDRATVNHSRIVHQVQLYGNATITHAFIEHRAEVFDFALIEGDKDNNVWICDCAKVYGHARVIAGTEEDAIPTLRYSSQVAEHALIEGNCVLKHHVLVGGHAEVRGGPILLDDRVLIEGHACIQGEILIERQVEISGRAAVIAFDDNTIHLRGPKVINGEDRITRT 320
               SCOP domains d2piga_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....eeeeeee..eeeeeeeeeeee...........eeeee............ee.....eee...ee....eee...eee...ee....eee..eee...ee....eee..eee..eee....eee...eee.--------...eee....eee..eee...ee....eee.eee....ee....eee......eee....ee....eee.........ee....ee....eee..eee...eee....eee...eeee..eee....eee..eeee..eee....eee......eeee..eee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pig A   3 KYRLSEGPRAFTYQVDGEKKSVLLRQVIAVTDFNDVKAGTSGGWVDADNVLSQQGDCWIYDENAmAFAGTEITGNARITQPCTLYNNVRIGDNVWIDRADISDGARISDNVTIQSSSVREECAIYGDARVLNQSEILA--------AQILQIYDRATVNHSRIVHQVQLYGNATITHAFIEHRAEVFDFALIEGDKDNNVWICDCAKVYGHARVIAGTEEDAIPTLRYSSQVAEHALIEGNCVLKHHVLVGGHAEVRGGPILLDDRVLIEGHACIQGEILIERQVEISGRAAVIAFDDNTIHLRGPKVINGEDRITRT 320
                                    12        22        32        42        52        62    |   72        82        92       102       112       122       132       | -      |152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312        
                                                                                           67-MSE                                                                  140      149                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with A0A0H2WQ05_S | A0A0H2WQ05 from UniProtKB/TrEMBL  Length:326

    Alignment length:328
                                                                                                                                                                                                                                                                                                                                                             326    
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   |    
         A0A0H2WQ05_S     3 KYRLSEGPRAFTYQVDGEKKSVLLRQVIAVTDFNDVKAGTSGGWVDADNVLSQQGDCWIYDENAMAFAGTEITGNARITQPCTLYNNVRIGDNVWIDRADISDGARISDNVTIQSSSVREECAIYGDARVLNQSEILAIQGLTHEHAQILQIYDRATVNHSRIVHQVQLYGNATITHAFIEHRAEVFDFALIEGDKDNNVWICDCAKVYGHARVIAGTEEDAIPTLRYSSQVAEHALIEGNCVLKHHVLVGGHAEVRGGPILLDDRVLIEGHACIQGEILIERQVEISGRAAVIAFDDNTIHLRGPKVINGEDRITRTPLVGSL----   -
               SCOP domains d2pigb_ B: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeeee..eeeeeeeeeeee...........eeeee............ee.....eee...ee....eee...eee...ee....eee..eee...ee....eee..eee..eee....eee...eeee.--------..eee....eee..eeee..ee....eee.eee....ee....eee......eee....ee....eee.........ee....ee....eee..eee...eee....eee...eeee..eee....eee..eeee..eee....eee...-..eeee..eee....ee.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pig B   3 KYRLSEGPRAFTYQVDGEKKSVLLRQVIAVTDFNDVKAGTSGGWVDADNVLSQQGDCWIYDENAmAFAGTEITGNARITQPCTLYNNVRIGDNVWIDRADISDGARISDNVTIQSSSVREECAIYGDARVLNQSEILAI--------QILQIYDRATVNHSRIVHQVQLYGNATITHAFIEHRAEVFDFALIEGDKDNNVWICDCAKVYGHARVIAGTEEDAIPTLRYSSQVAEHALIEGNCVLKHHVLVGGHAEVRGGPILLDDRVLIEGHACIQGEILIERQVEISGRAAVIAFD-NTIHLRGPKVINGEDRITRTPLVGSLLEHH 330
                                    12        22        32        42        52        62    |   72        82        92       102       112       122       132        |-       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      |302       312       322        
                                                                                           67-MSE                                                                   141      150                                                                                                                                                  299 |                             
                                                                                                                                                                                                                                                                                                                                    301
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PIG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PIG)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2PIG)

 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 ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:261 - Pro A:262   [ RasMol ]  
    Gly A:307 - Pro A:308   [ RasMol ]  
    Gly B:261 - Pro B:262   [ RasMol ]  
    Gly B:307 - Pro B:308   [ RasMol ]  
 

(-) 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
  2pig
    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
  A0A0H2WQ05_S | A0A0H2WQ05
    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
  A0A0H2WQ05_S | A0A0H2WQ05
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2WQ05_S | A0A0H2WQ05: 2f9c

(-) Related Entries Specified in the PDB File

2f9c THE SAME PROTEIN AT LOWER RESOLUTION
scr6