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 PROTEIN OF UNKNOWN FUNCTION YHAL FROM BACILLUS SUBTILIS
 
Authors :  Y. Kim, A. Joachimiak, E. Evdokimova, A. Savchenko, A. Edwards, Midwes For Structural Genomics (Mcsg)
Date :  17 Feb 04  (Deposition) - 25 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Hypothetical Protein, Yhai, Four Helix Bundle, Colied-Coil, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, A. Joachimiak, E. Evdokimova, A. Savchenko, A. Edwards
The Crystal Structure Of The Hypothetical Protein Yhai, Apc1180 From Bacillus Subtilis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YHAI
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YHAI
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: APC1180

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 29)

Asymmetric/Biological Unit (4, 29)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MPD17Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA3Ligand/IonSODIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:52 , GLU A:55 , ASP C:107 , HIS C:111BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREASP A:107 , HIS A:111 , GLU B:52 , GLU B:55BINDING SITE FOR RESIDUE ZN B 502
03AC3SOFTWAREASP B:107 , HIS B:111 , GLU C:52 , GLU C:55BINDING SITE FOR RESIDUE ZN C 503
04AC4SOFTWAREGLY A:77 , GOL A:801 , GOL A:802 , HOH A:875BINDING SITE FOR RESIDUE NA A 504
05AC5SOFTWAREGLY B:77 , GOL B:803 , GOL B:804 , HOH B:869BINDING SITE FOR RESIDUE NA B 505
06AC6SOFTWAREGLY C:77 , GOL C:805 , GOL C:806BINDING SITE FOR RESIDUE NA C 506
07AC7SOFTWAREASP A:51 , HOH A:864 , HIS C:111 , HOH C:824BINDING SITE FOR RESIDUE MPD A 701
08AC8SOFTWAREASP A:69 , ALA A:73 , MPD A:715BINDING SITE FOR RESIDUE MPD A 702
09AC9SOFTWAREVAL A:85 , MET A:109 , PHE A:112 , ASP A:113BINDING SITE FOR RESIDUE MPD A 703
10BC1SOFTWAREHIS A:111 , PHE A:112 , HOH A:856 , MET B:47 , ASP B:51 , HOH B:865BINDING SITE FOR RESIDUE MPD B 704
11BC2SOFTWAREASP B:69 , PHE B:112BINDING SITE FOR RESIDUE MPD B 705
12BC3SOFTWAREALA B:76 , VAL B:85 , HIS B:86 , PHE B:112 , ASP B:113BINDING SITE FOR RESIDUE MPD B 706
13BC4SOFTWAREARG A:10 , GLN C:16 , ILE C:34BINDING SITE FOR RESIDUE MPD C 707
14BC5SOFTWAREHIS B:111 , PHE B:112 , HOH B:822 , MET C:47 , ASP C:51 , HOH C:820BINDING SITE FOR RESIDUE MPD C 708
15BC6SOFTWAREALA C:76 , HIS C:86 , PHE C:112 , ASP C:113 , MPD C:710BINDING SITE FOR RESIDUE MPD C 709
16BC7SOFTWAREASP C:69 , ALA C:73 , PHE C:112 , MPD C:709BINDING SITE FOR RESIDUE MPD C 710
17BC8SOFTWARELYS B:61 , HOH B:830 , GLU C:56 , HOH C:880BINDING SITE FOR RESIDUE MPD C 711
18BC9SOFTWAREGLU A:56 , HOH A:862 , VAL C:66 , HOH C:833BINDING SITE FOR RESIDUE MPD A 712
19CC1SOFTWAREGLN B:16 , ILE B:34 , ASP B:35 , ARG C:10BINDING SITE FOR RESIDUE MPD B 713
20CC2SOFTWARELYS A:70 , LYS C:61 , ALA C:62 , GLY C:64BINDING SITE FOR RESIDUE MPD A 714
21CC3SOFTWAREASP A:69 , LYS A:70 , ALA A:73 , MPD A:702BINDING SITE FOR RESIDUE MPD A 715
22CC4SOFTWARELYS A:61 , ALA A:62 , GLN A:63 , GLY A:64 , LYS B:70BINDING SITE FOR RESIDUE MPD B 716
23CC5SOFTWARELYS B:61 , ALA B:62 , GLY B:64 , LYS C:70 , LEU C:74BINDING SITE FOR RESIDUE MPD C 717
24CC6SOFTWAREALA A:76 , GLY A:77 , LEU A:79 , NA A:504 , HOH A:874BINDING SITE FOR RESIDUE GOL A 801
25CC7SOFTWAREGLY A:77 , GLN A:78 , NA A:504 , HOH A:874 , HOH A:875 , GLN C:63 , GLY C:64 , PHE C:65BINDING SITE FOR RESIDUE GOL A 802
26CC8SOFTWAREALA B:76 , GLY B:77 , LEU B:79 , NA B:505 , GOL B:804 , HOH B:882BINDING SITE FOR RESIDUE GOL B 803
27CC9SOFTWAREGLN A:63 , GLY A:64 , PHE A:65 , GLY B:77 , NA B:505 , GOL B:803 , HOH B:880 , HOH B:882BINDING SITE FOR RESIDUE GOL B 804
28DC1SOFTWAREALA C:76 , GLY C:77 , LEU C:79 , GLU C:81 , NA C:506 , HOH C:808 , HOH C:822BINDING SITE FOR RESIDUE GOL C 805
29DC2SOFTWAREGLN B:63 , GLY B:64 , PHE B:65 , GLY C:77 , GLN C:78 , NA C:506 , HOH C:807 , HOH C:822BINDING SITE FOR RESIDUE GOL C 806

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SED)

(-) 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:112
 aligned with YHAI_BACSU | O07517 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:112
                                    11        21        31        41        51        61        71        81        91       101       111  
           YHAI_BACSU     2 DSMDHRIERLEYYIQLLVKTVDMDRYPFYALLIDKGLSKEEGEAVMRICDELSEELATQKAQGFVTFDKLLALFAGQLNEKLDVHETIFALYEQGLYQELMEVFIDIMKHFD 113
               SCOP domains d1seda_ A: Hypothetical protein YhaI                                                                             SCOP domains
               CATH domains 1sedA00 A:2-113 Hypothetical protein YhaI like domains                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1sed A   2 DSMDHRIERLEYYIQLLVKTVDMDRYPFYALLIDKGLSKEEGEAVMRICDELSEELATQKAQGFVTFDKLLALFAGQLNEKLDVHETIFALYEQGLYQELMEVFIDIMKHFD 113
                                    11        21        31        41        51        61        71        81        91       101       111  


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with YHAI_BACSU | O07517 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:110
                                    13        23        33        43        53        63        73        83        93       103       113
           YHAI_BACSU     4 MDHRIERLEYYIQLLVKTVDMDRYPFYALLIDKGLSKEEGEAVMRICDELSEELATQKAQGFVTFDKLLALFAGQLNEKLDVHETIFALYEQGLYQELMEVFIDIMKHFD 113
               SCOP domains d1sedb_ B: Hypothetical protein YhaI                                                                           SCOP domains
               CATH domains 1sedB00 B:4-113 Hypothetical protein YhaI like domains                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1sed B   4 MDHRIERLEYYIQLLVKTVDMDRYPFYALLIDKGLSKEEGEAVMRICDELSEELATQKAQGFVTFDKLLALFAGQLNEKLDVHETIFALYEQGLYQELMEVFIDIMKHFD 113
                                    13        23        33        43        53        63        73        83        93       103       113


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with YHAI_BACSU | O07517 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:112
                                    11        21        31        41        51        61        71        81        91       101       111  
           YHAI_BACSU     2 DSMDHRIERLEYYIQLLVKTVDMDRYPFYALLIDKGLSKEEGEAVMRICDELSEELATQKAQGFVTFDKLLALFAGQLNEKLDVHETIFALYEQGLYQELMEVFIDIMKHFD 113
               SCOP domains d1sedc_ C: Hypothetical protein YhaI                                                                             SCOP domains
               CATH domains 1sedC00 C:2-113 Hypothetical protein YhaI like domains                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1sed C   2 DSMDHRIERLEYYIQLLVKTVDMDRYPFYALLIDKGLSKEEGEAVMRICDELSEELATQKAQGFVTFDKLLALFAGQLNEKLDVHETIFALYEQGLYQELMEVFIDIMKHFD 113
                                    11        21        31        41        51        61        71        81        91       101       111
   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  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sed)
 

(-) 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
  1sed
    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
  YHAI_BACSU | O07517
    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
  YHAI_BACSU | O07517
    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 1SED)

(-) Related Entries Specified in the PDB File

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