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 PRE-SPECIFIC RESTRICTION ENDONUCLEASE AGEI-DNA COMPLEX
 
Authors :  G. Tamulaitiene, V. Jovaisaite, S. Grazulis, V. Siksnys
Date :  22 Sep 15  (Deposition) - 05 Oct 16  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Restriction Endonuclease, Pd-(D/E)Xk Nuclease, Protein-Dna Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Tamulaitiene, V. Jovaisaite, G. Tamulaitis, I. Songailiene, E. Manakova, M. Zaremba, S. Grazulis, S. Y. Xu, V. Siksnys
Restriction Endonuclease Agei Is A Monomer Which Dimerizes To Cleave Dna.
Nucleic Acids Res. V. 45 3547 2017
PubMed-ID: 28039325  |  Reference-DOI: 10.1093/NAR/GKW1310

(-) Compounds

Molecule 1 - TYPE-2 RESTRICTION ENZYME AGEI
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRRS-AGEIRM
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AGEIR
    Organism Scientific: THALASSOBIUS GELATINOVORUS
    Organism Taxid: 53501
    Synonym: R.AGEI,ENDONUCLEASE AGEI,TYPE II RESTRICTION ENZYME AGEI
 
Molecule 2 - DNA (5'-D(*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*G*)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5DWA)

(-) Sites  (0, 0)

(no "Site" information available for 5DWA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DWA)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:204 -Pro A:205
2Arg B:9 -Gly B:10
3Pro B:204 -Pro B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DWA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DWA)

(-) Exons   (0, 0)

(no "Exon" information available for 5DWA)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...........eeeeee..........eeeeeeeeee....hhhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhh.....eeee.................eee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwa A   1 MRLDLDFGRGLVAHVMLDNVSEEQYQQISDYFVPLVNKPKLKSRDAIGQAFVMATEVCPDANPSDLWHHVLYRIYIREKIGTDPSQSWVRTSGEAFEVALVERYNPVLARHGIRLTALFKGQKGLALTRMGVADRVGSRKVDVMIEKQGGGRSPDAEGFGVVGGIHAKVSLAERVSDDIPASRIMMGEGLLSVLSTLDVKSFPPPHGDLVNRGELGTPDRPSDKRNYIEGHGDFSACFSYNLRTSPSNATTPSGRHIYVSGFSGQDDEFTDYLVAQLA 278
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh......hhhhh.eeeeee..........eeeeeeeeee.....hhhhhhhhhhhhhhh..eeeeee.........................hhhhhhhhh.....eeee.................eee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwa B   1 MRLDLDFGRGLVAHVMLDNVSEEQYQQISDYFVPLVNKPKLKSRDAIGQAFVMATEVCPDANPSDLWHHVLYRIYIREKIGTDPSQSWVRTSGEAFEVALVERYNPVLARHGIRLTALFKGQKGLALTRMGVADRVGSRKVDVMIEKQGGGRSPDAEGFGVVGGIHAKVSLAERVSDDIPASRIMMGEGLLSVLSTLDVKSFPPPHGDLVNRGELGTPDRPSDKRNYIEGHGDFSACFSYNLRTSPSNATTPSGRHIYVSGFSGQDDEFTDYLVAQLA 278
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270        


Chain C from PDB  Type:DNA  Length:11
                                           
                 5dwa C  -2 TCGACCGGTCG   8
                                     7 


Chain D from PDB  Type:DNA  Length:11
                                           
                 5dwa D  -2 TCGACCGGTCG   8
                                     7
   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 5DWA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DWA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DWA)

(-) Gene Ontology  (6, 6)

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
(no "Ligands, Modified Residues, Ions" information available for 5dwa)
 
  Sites
(no "Sites" information available for 5dwa)
 
  Cis Peptide Bonds
    Arg B:9 - Gly B:10   [ RasMol ]  
    Pro A:204 - Pro A:205   [ RasMol ]  
    Pro B:204 - Pro B:205   [ 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 ](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
  5dwa
    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
  T2A1_THAGE | Q9KHV6
    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)
  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
  T2A1_THAGE | Q9KHV6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        T2A1_THAGE | Q9KHV6: 5dwb 5dwc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DWA)