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 AN UNCHARACTERIZED PROTEIN (YNCM) FROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 AT 1.55 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Oct 12  (Deposition) - 05 Dec 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peptidase A4-Like Fold, Yrpd, Pf15493 Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of An Uncharacterized Protein (Yncm) From Bacillus Subtilis Subsp. Subtilis Str. 168 At 1. 55 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YNCM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSU17690, NP_389652.1, YNCM
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:58 , TYR A:60 , GLU A:100 , LYS A:191 , HOH A:628 , HOH A:643BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARELYS A:115 , TYR A:128 , THR A:136 , TYR A:137 , HOH A:626 , HOH A:639 , LYS B:132 , ASP B:133 , SER B:202BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREARG B:58 , TYR B:60 , GLU B:100 , LYS B:191 , HOH B:479 , HOH B:589 , HOH B:610BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWARELYS A:132 , ASP A:133 , HOH A:528 , LYS B:115 , THR B:136 , TYR B:137 , HOH B:604 , HOH B:605BINDING SITE FOR RESIDUE SO4 B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HFS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HFS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HFS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HFS)

(-) Exons   (0, 0)

(no "Exon" information available for 4HFS)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeee............eeeeeeeeee....eeeeeeeee....eeeeeeee......eeeehhhhhh.........eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeeeeee..hhhhhhhh.eeeeeeeeeeee..ee...eeeeee.eeeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hfs A  48 ASELPNGIGGRVYLNSTGAVFTAKIVLPETVKNNDSVSTPYIYSGFRATSGTEADIGLQYSKQYNVWKPLmKVGSKNEETYIEGKDKFTYNKGFRPGSTVQmTIYKNLSGNTRmTLWGTNNDGYTGRIITEIQGTNIGTISKWKTLATAAVSYESQRDAIKATFSTSFNNITIDNKAVTPVVDTQDFAKVSVAGNNVTISVNK 250
                                    57        67        77        87        97       107       117|      127       137       147 |     157   |   167       177       187       197       207       217       227       237       247   
                                                                                                118-MSE                        149-MSE     161-MSE                                                                                     


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeee............eeeeeeeeee....eeeeeeeee....eeeeeeee......eeeehhhhhh.........eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeeeeee..hhhhhh...eeeeeeeeeeee..ee...eeeeee.eeeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hfs B  48 ASELPNGIGGRVYLNSTGAVFTAKIVLPETVKNNDSVSTPYIYSGFRATSGTEADIGLQYSKQYNVWKPLmKVGSKNEETYIEGKDKFTYNKGFRPGSTVQmTIYKNLSGNTRmTLWGTNNDGYTGRIITEIQGTNIGTISKWKTLATAAVSYESQRDAIKATFSTSFNNITIDNKAVTPVVDTQDFAKVSVAGNNVTISVNK 250
                                    57        67        77        87        97       107       117|      127       137       147 |     157   |   167       177       187       197       207       217       227       237       247   
                                                                                                118-MSE                        149-MSE     161-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 4HFS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HFS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HFS)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 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 ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hfs)
 

(-) 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
  4hfs
    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
  YNCM_BACSU | O31803
    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
  YNCM_BACSU | O31803
    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 4HFS)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HFS)