Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE MEMBER OF THE DINB FAMILY (EXIG_1237) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Jul 06  (Deposition) - 15 Aug 06  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative Member Of The Dinb Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Conserved Hypothetical Protein Rbl0055 (Zp_00537729. 1) From Exiguobacterium Sp. 255-15 At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ZP_00537729.1
    Organism Scientific: EXIGUOBACTERIUM SIBIRICUM
    Organism Taxid: 262543
    Strain: 255-15

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:48 , HIS A:123 , HIS A:127 , CL A:152 , HOH A:153 , HOH A:155BINDING SITE FOR RESIDUE NI A 149
2AC2SOFTWAREARG A:40 , GLN A:130BINDING SITE FOR RESIDUE CL A 150
3AC3SOFTWAREHIS A:123 , HIS A:127 , NI A:149 , HOH A:153 , HOH A:154 , HOH A:155BINDING SITE FOR RESIDUE CL A 152

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HKV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HKV)

(-) Sequences/Alignments

Asymmetric 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:148
 aligned with B1YEV7_EXIS2 | B1YEV7 from UniProtKB/TrEMBL  Length:148

    Alignment length:148
                             1                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139        
         B1YEV7_EXIS2     - -MTDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFYAVPVLPEQLVDRLDQSWQYYQDRLMADFSTETTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIKLDLF 147
               SCOP domains -d2hkva1 A:1-147 Hypothetical protein ExigDRAFT_2445                                                                                                 SCOP domains
               CATH domains 2hkvA01 A:0-140 dinb family like domain                                                                                                      ------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkv A   0 GmTDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEmAQFYAVPVLPEQLVDRLDQSWQYYQDRLmADFSTETTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIKLDLF 147
                             |       9        19        29        39        49        59        69        79        89       |99       109       119       129       139        
                             |                                                                 68-MSE                       97-MSE                                              
                             1-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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 Visualization

(-) Interactive Views

Asymmetric 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hkv)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2hkv
    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
  B1YEV7_EXIS2 | B1YEV7
    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
  B1YEV7_EXIS2 | B1YEV7
    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 2HKV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2HKV)