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

(-) Description

Title :  CRYSTAL STRUCTURE OF R-PROTEIN OF NGOAVII RESTRICTION ENDONUCLEASE
 
Authors :  G. Tamulaitiene, A. Silanskas, S. Grazulis, M. Zaremba, V. Siksnys
Date :  17 Sep 14  (Deposition) - 24 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Restriction Endonuclease, B3 Domain, Pld Nuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Tamulaitiene, A. Silanskas, S. Grazulis, M. Zaremba, V. Siksnys
Crystal Structure Of The R-Protein Of The Multisubunit Atp-Dependent Restriction Endonuclease Ngoavii.
Nucleic Acids Res. V. 42 14022 2014
PubMed-ID: 25429979  |  Reference-DOI: 10.1093/NAR/GKU1237

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE R.NGOVII
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NGK_0521, NGO0364
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 242231
    Strain: ATCC 700825 / FA 1090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 4RCT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RCT)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........hhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee.........eeeeee..eeeeeee................eeeeeehhhhhhhhhhhhhhhhhhhee.hhh...........hhhhh...ee.hhhhhhhhhhh....eeeee......hhhhhhhh..ee.....ee........ee.hhhhhh........eeeeee...eeeeeeeehhhh.eeee....hhhhhhhhhhhhhh.........hhhhhhhhh..eeeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rct A  -1 SHMNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKIDLLVGMHYLEGFSHLQYDSLcKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLIGSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSHLENcLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWYEVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKNFRSENDLKTLGKWIKGRLESHGCLQNNEKITHETLREYGNDHFELRSTDNPDVWLLSFKGKN 345
                                     8        18        28        38        48        58        68        78  |     88        98       108       118       128       138       148       158       168       178     | 188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       
                                                                                                             81-CME                                                                                                184-CME                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........hhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh....eeeeee.hhhhhh.hhhhhhhhhhhhhhhhhhh.eeeee.........eeeeee..eeeeeee................eeeeeehhhhhhhhhhhhhhhhhhhee.hhh...........hhhhh...ee.hhhhhhhhhhh....eeeee......hhhhhhhh..ee.....ee........ee.hhhhhh........eeeeee...eeeeeeeehhhh.eeee....hhhhhhhhhhhhhh.........hhhhhhhhh..eeeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rct B  -1 SHMNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKIDLLVGMHYLEGFSHLQYDSLcKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLIGSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSHLENcLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWYEVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKNFRSENDLKTLGKWIKGRLESHGCLQNNEKITHETLREYGNDHFELRSTDNPDVWLLSFKGKN 345
                                     8        18        28        38        48        58        68        78  |     88        98       108       118       128       138       148       158       168       178     | 188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       
                                                                                                             81-CME                                                                                                184-CME
   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 4RCT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    CME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4rct)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rct)
 

(-) 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 ](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
  4rct
    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
  Q5F9M9_NEIG1 | Q5F9M9
    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)
  3.1.21.4
    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
  Q5F9M9_NEIG1 | Q5F9M9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5F9M9_NEIG1 | Q5F9M9: 4rd5 4rdm

(-) Related Entries Specified in the PDB File

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