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
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)

(-) Description

Title :  STRUCTURE OF 5-CHLOROURACIL MODIFIED A:U BASE PAIR
 
Authors :  A. Patra, M. Egli
Date :  01 Nov 12  (Deposition) - 19 Dec 12  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  5-Chloro-2'-Deoxyuridine, W-C Base Pair, Wobble Base Pair, Double Helix, Base Pairing Pattern, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Patra, J. Harp, P. S. Pallan, L. Zhao, M. Abramov, P. Herdewijn, M. Egli
Structure, Stability And Function Of 5-Chlorouracil Modifie A:U And G:U Base Pairs.
Nucleic Acids Res. V. 41 2689 2013
PubMed-ID: 23275540  |  Reference-DOI: 10.1093/NAR/GKS1316

(-) Compounds

Molecule 1 - RIBONUCLEASE H
    Chains: A, B
    EC Number: 3.1.26.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RNHA, BH0863
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
    Synonym: RNASE H
 
Molecule 2 - DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(UCL)P*CP*GP*CP*G)-3')
    Chains: C, D, E, F
    Engineered: YES
    Other Details: CLU8
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL3Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4UCL4Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4UCL2Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4UCL2Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , GLU A:109 , ASN A:132 , HOH A:340 , HOH A:426 , HOH A:440 , HOH A:441BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREGLY A:76 , ASN A:77 , PRO A:78 , HOH A:345 , THR B:176 , PRO B:177 , ILE B:178 , HOH B:341 , HOH B:377 , HOH B:441BINDING SITE FOR RESIDUE GOL B 201
3AC3SOFTWARETHR A:135 , HOH A:492 , DG C:2 , HOH C:203 , HOH C:204 , HOH C:205 , HOH C:218 , DG D:22 , DC D:23 , DG D:24 , HOH D:104BINDING SITE FOR RESIDUE GOL C 101
4AC4SOFTWAREDG E:2 , HOH E:207 , HOH E:213 , HOH E:215 , HOH E:217 , HOH F:206BINDING SITE FOR RESIDUE MG E 101
5AC5SOFTWARELYS A:143 , THR A:173 , TYR A:174 , DG F:24 , HOH F:203 , HOH F:218BINDING SITE FOR RESIDUE GOL F 101
6AC6SOFTWARELYS A:141 , DG E:2 , DC E:3 , HOH E:217 , DG F:22 , HOH F:211 , HOH F:212 , HOH F:216BINDING SITE FOR RESIDUE EDO F 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:77 -Pro A:78
2Glu B:61 -Glu B:62
3Asn B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HTU)

(-) 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:134
                                                                                                                                                                      
               SCOP domains d4htua_ A: BH0863-like Ribonuclease H                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....eee.hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4htu A  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
                                    70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4htub_ B: BH0863-like Ribonuclease H                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee...eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4htu B  61 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADYG 194
                                    70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain C from PDB  Type:DNA  Length:12
                                            
                 4htu C   1 CGCGAATxCGCG  12
                                   |10  
                                   8-UCL


Chain D from PDB  Type:DNA  Length:12
                                            
                 4htu D  13 CGCGAATxCGCG  24
                                   |22  
                                  20-UCL


Chain E from PDB  Type:DNA  Length:8
                                        
                 4htu E   1 CGCGAATx   8
                                   |
                                   8-UCL


Chain F from PDB  Type:DNA  Length:9
                                         
                 4htu F  16 GAATxCGCG  24
                                |    
                                |    
                               20-UCL
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UCL  [ 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 ]
 
  Cis Peptide Bonds
    Asn A:77 - Pro A:78   [ RasMol ]  
    Asn B:77 - Pro B:78   [ RasMol ]  
    Glu B:61 - Glu B:62   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  4htu
    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
  RNH1_BACHD | Q9KEI9
    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)
  3.1.26.4
    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
  RNH1_BACHD | Q9KEI9
    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
        RNH1_BACHD | Q9KEI9: 1zbf 1zbi 1zbl 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w 2r7y 3d0p 3ey1 3i8d 3twh 3uld 4hue 4huf 4hug 4opj 4opk 5swm 5us2 5usa 5use 5usg 5w7n 5w7o

(-) Related Entries Specified in the PDB File

4hue 4huf 4hug