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 :  K262A MUTANT OF I-SMAMI
 
Authors :  B. Shen, B. Stoddard
Date :  09 Oct 15  (Deposition) - 13 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Laglidadg, I-Smami, K262A, Mutant, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Shen, A. Lambert, B. C. Walker, B. L. Stoddard, B. K. Kaiser
The Structural Basis Of Asymmetry In Dna Binding And Cleavage As Exhibited By The I-Smami Laglidadg Meganuclease
J. Mol. Biol. V. 428 206 2016
PubMed-ID: 26705195  |  Reference-DOI: 10.1016/J.JMB.2015.12.005

(-) Compounds

Molecule 1 - I-SMAMI LAGLIDADG MEGANUCLEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 114-415
    Gene: SMAC_12671
    Mutation: YES
    Organism Scientific: SORDARIA MACROSPORA (STRAIN ATCC MYA-333 / DSM 997 / K(L3346) / K-HELL)
    Organism Taxid: 771870
    Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-HELL
 
Molecule 2 - DNA RIGHT HALF SITE BOTTOM STRAND
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA LEFT HALF SITE BOTTOM STRAND
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA LEFT SITE TOP STRAND
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 5 - DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2MXE1Ligand/Ion2-METHOXYETHANOL
3PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:19 , GLU A:20 , ASP A:179 , MG A:402 , DA B:14 , DT C:15 , DT D:15 , DC E:16binding site for residue MG A 401
2AC2SOFTWAREALA A:19 , ASP A:179 , MG A:401 , DT C:15 , DT D:15 , HOH D:101binding site for residue MG A 402
3AC3SOFTWAREGLU A:20 , SER A:177 , GLY A:178 , DA B:14 , DC E:16binding site for residue MG A 403
4AC4SOFTWARELYS A:49 , DC C:25 , DG D:1binding site for residue MXE A 404
5AC5SOFTWAREDG B:2 , DT B:3 , DC E:24 , DG E:25binding site for residue PG0 E 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E63)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:299 -Gly A:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E63)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E63)

(-) Exons   (0, 0)

(no "Exon" information available for 5E63)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhh....eeee....eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.................hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee.....eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e63 A   8 LNPWAVVGFIDAEGSFMVRVRKNSKYKTGWLVVAIFSVTVDKKDLFLLESLKTFFGGLGSIKKSGNSTFSYRIESSEQLTKIILPFFDKYSLITEKLGDYLLFKKVLELMGTKEHLTQRGLEKIVSLKASINKGLSEELQAAFPQCVPTPRPEINNKNIPDPFWLAGFVSGDGSFKSILKKSESIKVGFQSILVFQITQHARDVKLMESLISYLGCGFIEKDSRGPWLYYTVTNFSDIQGKIIPFFHQYKIIGSAYGDYQDWCKIALIMQNKNHLTPEGLNEIRALKGGMNKG 300
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297   


Chain B from PDB  Type:DNA  Length:14
                                              
                 5e63 B   1 CGTACACCTGATAA  14
                                    10    


Chain C from PDB  Type:DNA  Length:11
                                           
                 5e63 C  15 TGGAGGATACC  25
                                    24 


Chain D from PDB  Type:DNA  Length:15
                                               
                 5e63 D   1 GGTATCCTCCATTAT  15
                                    10     


Chain E from PDB  Type:DNA  Length:10
                                          
                 5e63 E  16 CAGGTGTACG  25
                                    25
   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 5E63)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E63)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E63)

(-) Gene Ontology  (3, 3)

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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MXE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG0  [ 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 ]
 
  Cis Peptide Bonds
    Lys A:299 - Gly A:300   [ 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 | 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
  5e63
    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
  F7WD42_SORMK | F7WD42
    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
  F7WD42_SORMK | F7WD42
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        F7WD42_SORMK | F7WD42: 4lox 4z1z 4z20 5e5o 5e5p 5e5s 5e67

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E63)