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 PUTATIVE UNCHARACTERIZED PROTEIN FROM JONESIA DENITRIFICANS
 
Authors :  C. Chang, L. Volkart, J. Bearden, D. Wu, J. Eisen, C. Kerfeld, A. Joachim Midwest Center For Structural Genomics (Mcsg)
Date :  26 Feb 10  (Deposition) - 09 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Jonesia Denitrificans, Psi-2, Mcsg, Geba, Genomic Encyclopaedia Of Bacteria And Archaea, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, L. Volkart, J. Bearden, D. Wu, J. Eisen, C. Kerfeld, A. Joachimiak
Crystal Structure Of Putative Uncharacterized Protein From Jonesia Denitrificans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PMCSG19
    Gene: JDEN_0139
    Organism Scientific: JONESIA DENITRIFICANS
    Organism Taxid: 471856
    Strain: ATCC 14870 / DSM 20603 / CIP 55134

 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
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:86 , HOH A:180 , HOH A:269 , HOH A:294 , HOH A:349 , HOH A:361BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREASP A:90 , HOH A:227 , HOH A:253 , HOH A:382 , HOH A:424 , HOH B:263 , HOH B:292BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWARETHR A:87 , THR A:88 , HOH A:461 , ASP B:78BINDING SITE FOR RESIDUE EDO A 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:6 -Pro A:7
2Tyr B:6 -Pro B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LYD)

(-) 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 C7QYG7_JONDD | C7QYG7 from UniProtKB/TrEMBL  Length:158

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         C7QYG7_JONDD     1 MPSIRYPSTEFPALTGFTVPIPETWQPDPTMGTQFAARPHTPPQGFTPNIIGTVRRAATGALHNQRTELDQRATQLPDYAERGRTETTVDGFPAYHIEYAYRHHGTITIAQMITLVEVSHPHAVDIIQLTATCAGDQTADYWDTFRLMHADLTVQPHG 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........eeeee....eee.......eeeee.........eeeeeeeee..hhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeee..hhhhhhhhhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lyd A   1 mPSIRYPSTEFPALTGFTVPIPETWQPDPTmGTQFAARPHTPPQGFTPNIIGTVRRAATGALHNQRTELDQRATQLPDYAERGRTETTVDGFPAYHIEYAYRHHGTITIAQmITLVEVSHPHAVDIIQLTATCAGDQTADYWDTFRLmHADLTVQPHG 158
                            |       10        20        30|       40        50        60        70        80        90       100       110 |     120       130       140       150        
                            |                            31-MSE                                                                          112-MSE                             148-MSE      
                            1-MSE                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with C7QYG7_JONDD | C7QYG7 from UniProtKB/TrEMBL  Length:158

    Alignment length:160
                              1                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
         C7QYG7_JONDD     - --MPSIRYPSTEFPALTGFTVPIPETWQPDPTMGTQFAARPHTPPQGFTPNIIGTVRRAATGALHNQRTELDQRATQLPDYAERGRTETTVDGFPAYHIEYAYRHHGTITIAQMITLVEVSHPHAVDIIQLTATCAGDQTADYWDTFRLMHADLTVQPHG 158
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------DUF1795-3lydB01 B:52-152                                                                             ------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------DUF1795-3lydB02 B:52-152                                                                             ------ Pfam domains (2)
         Sec.struct. author ....eeee.........eeeee....eee.......eeeee.........eeeeeeeee..hhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeee..hhhhhhhhhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lyd B  -1 NAmPSIRYPSTEFPALTGFTVPIPETWQPDPTmGTQFAARPHTPPQGFTPNIIGTVRRAATGALHNQRTELDQRATQLPDYAERGRTETTVDGFPAYHIEYAYRHHGTITIAQmITLVEVSHPHAVDIIQLTATCAGDQTADYWDTFRLmHADLTVQPHG 158
                              |      8        18        28  |     38        48        58        68        78        88        98       108   |   118       128       138       148       158
                              1-MSE                        31-MSE                                                                          112-MSE                             148-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 3LYD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF1795] (2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LYD)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:6 - Pro A:7   [ RasMol ]  
    Tyr B:6 - Pro B:7   [ 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
  3lyd
    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
  C7QYG7_JONDD | C7QYG7
    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
  C7QYG7_JONDD | C7QYG7
    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 3LYD)

(-) Related Entries Specified in the PDB File

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