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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  RESTRICTION/MODIFICATION SYSTEM-TYPE II R-SWAI COMPLEXED WITH PARTIALLY CLEAVED DNA
 
Authors :  B. W. Shen, B. L. Stoddard
Date :  28 Sep 16  (Deposition) - 21 Dec 16  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,H,I,J,K
Biol. Unit 1:  A,B,C,D,H,I,J,K  (1x)
Biol. Unit 2:  A,B,H,I  (1x)
Biol. Unit 3:  C,D,J,K  (1x)
Keywords :  R-Swai, Uncleaved Dna Complex, R/M System, Rare Cutter, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Shen, D. F. Heiter, K. D. Lunnen, G. G. Wilson, B. L. Stoddard
Dna Recognition By The Swai Restriction Endonuclease Involves Unusual Distortion Of An 8 Base Pair A:T-Rich Target.
Nucleic Acids Res. V. 45 1516 2017
PubMed-ID: 28180307  |  Reference-DOI: 10.1093/NAR/GKW1200

(-) Compounds

Molecule 1 - R-SWAI PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: ER2566
    Expression System Plasmid: PHKT7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: STAPHYLOCOCCUS WARNERI
    Organism Taxid: 1292
    Other Details: SEMET INCORPORATED
 
Molecule 2 - DNA (26-MER)
    Chains: H, J
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: I, K
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDHIJK
Biological Unit 1 (1x): ABCDHIJK
Biological Unit 2 (1x): AB  HI  
Biological Unit 3 (1x):   CD  JK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric Unit (4, 27)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA4Ligand/IonCALCIUM ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 23)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:76 , ASP A:93 , PHE A:94 , HOH A:439 , DA H:25 , HOH H:202binding site for residue CA A 301
02AC2SOFTWAREGLY A:65 , ALA A:66 , PRO A:67 , TYR D:61 , ASP D:62binding site for residue EDO A 302
03AC3SOFTWAREGLU A:159 , SER A:160 , DG I:9 , DC I:10binding site for residue EDO A 303
04AC4SOFTWARESER A:160 , ARG A:162 , HOH A:427 , DG I:9 , DC I:10binding site for residue EDO A 304
05AC5SOFTWAREGLU A:69 , LYS D:82binding site for residue EDO A 305
06AC6SOFTWAREASP B:76 , ASP B:93 , PHE B:94 , HOH B:407 , HOH B:408 , DA I:25binding site for residue CA B 301
07AC7SOFTWAREPHE B:141binding site for residue ACT B 302
08AC8SOFTWAREASP C:76 , ASP C:93 , PHE C:94 , HOH C:409 , HOH C:413 , DA J:25binding site for residue CA C 301
09AC9SOFTWAREASP D:76 , ASP D:93 , PHE D:94 , HOH D:409 , HOH D:421 , DA K:25binding site for residue CA D 301
10AD1SOFTWAREGLU D:159 , SER D:160 , LYS D:192 , HOH D:414 , DC J:10binding site for residue EDO D 302
11AD2SOFTWARELYS A:72 , DA H:11 , DT H:12 , DG I:29 , DC I:30binding site for residue EDO H 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:166 -Pro A:167
2Lys B:166 -Pro B:167
3Lys C:166 -Pro C:167
4Lys D:166 -Pro D:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TGX)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeeeee...........eeeeeee..eeeeeeeeeeeee............hhhhhhhhhh...eeeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tgx A   2 NFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                                    11        21        31        41        51        61        71        81  |     91       101|      111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeeeee...........eeeeeee..eeeeeeeeeeeee...........hhhhhhhhhhh...eeeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tgx B   2 NFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                                    11        21        31        41        51        61        71        81  |     91       101|      111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain C from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeeeee...........eeeeeee..eeeeeeeeeeeee............hhhhhhhhhh....eeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tgx C   2 NFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                                    11        21        31        41        51        61        71        81  |     91       101|      111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeeeee...........eeeeeee..eeeeeeeeeeeee...........hhhhhhhhhhh....eeeeeeeeeee..eeee.......eeeee.hhh....eee...eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tgx D   2 NFKKYEENLVASIEEVIQRIIDDKHRPNIIGKTRVGAEVSDYLEDEFVKYISSGKSSSLYDAQGAPKEKTKNPWDARCKFKFmDREEEIWIDFKAFKITNmDSNPDIGTPNKIVKFIHEGNFYLVFVLVYYESKQDGVEFVKYNNDYKKVYLLKDVNESFRINPKPQmQVNIAAEPTYRTREEFIHFFVKKWKESFERQIKSLEKKEImLKDLEDKLKNSNDNSI 226
                                    11        21        31        41        51        61        71        81  |     91       101|      111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                                             84-MSE           102-MSE                                                            169-MSE                                  210-MSE            


Chain H from PDB  Type:DNA  Length:26
                                                          
                 5tgx H   2 GGCGGAGGCATTTAAATGCCGCGCGG  37
                                    11  ||    31      
                                       14|            
                                        25            


Chain I from PDB  Type:DNA  Length:26
                                                          
                 5tgx I   2 CCGCGCGGCATTTAAATGCCTCCGCC  37
                                    11  ||    31      
                                       14|            
                                        25            


Chain J from PDB  Type:DNA  Length:27
                                                           
                 5tgx J   1 GGGCGGAGGCATTTAAATGCCGCGCGG  37
                                    10   ||   30       
                                        14|            
                                         25            


Chain K from PDB  Type:DNA  Length:26
                                                          
                 5tgx K   2 CCGCGCGGCATTTAAATGCCTCCGCC  37
                                    11  ||    31      
                                       14|            
                                        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 5TGX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5TGX)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:166 - Pro A:167   [ RasMol ]  
    Lys B:166 - Pro B:167   [ RasMol ]  
    Lys C:166 - Pro C:167   [ RasMol ]  
    Lys D:166 - Pro D:167   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  5tgx
    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
  A0A1S4NYF7_S | A0A1S4NYF7
    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
  A0A1S4NYF7_S | A0A1S4NYF7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A1S4NYF7_S | A0A1S4NYF7: 5tgq 5th3

(-) Related Entries Specified in the PDB File

5tgq 5th3