Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  HIGH-RESOLUTION CRYSTAL STRUCTURE OF A FULLY MODIFIED N3'-> P5' PHOSPHORAMIDATE DNA DODECAMER DUPLEX
 
Authors :  V. Tereshko, S. Gryaznov, M. Egli
Date :  26 Nov 97  (Deposition) - 15 Dec 97  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  A-Dna, Modified, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Tereshko, S. Gryaznov, M. Egli
Consequences Of Replacing The Dna 3'-Oxygen By An Amino Group: High-Resolution Crystal Structure Of A Fully Modifie N3'--> P5' Phosphoramidate Dna Dodecamer Duplex
J. Am. Chem. Soc. V. 120 269 1998
PubMed: search

(-) Compounds

Molecule 1 - 5'-D(*(C42)P*(G38)P*(C42)P*(G38)P*(A43)P*(A43)P*(NYM) P*(NYM)P*(C42)P*(G38)P*(C42)P*DG)-3'
    Chains: A, B, C, D, E, F
    Engineered: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 102)

Asymmetric Unit (6, 102)
No.NameCountTypeFull Name
1A4312Mod. Nucleotide3'-AMINO DEOXYADENOSINE 5'-MONOPHOSPHATE
2C4224Mod. Nucleotide3'-AMINO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CL12Ligand/IonCHLORIDE ION
4G3818Mod. Nucleotide3'-AMINO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
5NH424Ligand/IonAMMONIUM ION
6NYM12Mod. Nucleotide3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE
Biological Unit 1 (5, 30)
No.NameCountTypeFull Name
1A434Mod. Nucleotide3'-AMINO DEOXYADENOSINE 5'-MONOPHOSPHATE
2C428Mod. Nucleotide3'-AMINO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4G386Mod. Nucleotide3'-AMINO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
5NH48Ligand/IonAMMONIUM ION
6NYM4Mod. Nucleotide3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE
Biological Unit 2 (5, 30)
No.NameCountTypeFull Name
1A434Mod. Nucleotide3'-AMINO DEOXYADENOSINE 5'-MONOPHOSPHATE
2C428Mod. Nucleotide3'-AMINO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4G386Mod. Nucleotide3'-AMINO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
5NH48Ligand/IonAMMONIUM ION
6NYM4Mod. Nucleotide3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE
Biological Unit 3 (5, 30)
No.NameCountTypeFull Name
1A434Mod. Nucleotide3'-AMINO DEOXYADENOSINE 5'-MONOPHOSPHATE
2C428Mod. Nucleotide3'-AMINO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4G386Mod. Nucleotide3'-AMINO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
5NH48Ligand/IonAMMONIUM ION
6NYM4Mod. Nucleotide3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG38 A:10 , C42 B:23BINDING SITE FOR RESIDUE NH4 A 226
02AC2SOFTWARECL A:250 , HOH A:318BINDING SITE FOR RESIDUE NH4 A 228
03AC3SOFTWAREC42 A:9 , NH4 A:228 , G38 B:22BINDING SITE FOR RESIDUE CL A 250
04AC4SOFTWAREA43 A:6 , NYM B:19BINDING SITE FOR RESIDUE NH4 B 225
05AC5SOFTWARECL B:249 , HOH B:317BINDING SITE FOR RESIDUE NH4 B 227
06AC6SOFTWAREA43 A:5 , A43 B:18 , NH4 B:227BINDING SITE FOR RESIDUE CL B 249
07AC7SOFTWAREA43 D:118 , A43 E:205BINDING SITE FOR RESIDUE NH4 E 229
08AC8SOFTWARECL E:251 , HOH E:361BINDING SITE FOR RESIDUE NH4 E 235
09AC9SOFTWAREA43 D:117 , G38 E:204 , NH4 E:235BINDING SITE FOR RESIDUE CL E 251
10BC1SOFTWAREG38 D:122 , C42 E:209BINDING SITE FOR RESIDUE NH4 E 230
11BC2SOFTWARECL E:252 , HOH E:360BINDING SITE FOR RESIDUE NH4 E 234
12BC3SOFTWAREC42 D:121 , NYM E:208 , NH4 E:234BINDING SITE FOR RESIDUE CL E 252
13BC4SOFTWAREC42 C:111 , DG F:224BINDING SITE FOR RESIDUE NH4 F 232
14BC5SOFTWARENYM C:107 , NYM F:220BINDING SITE FOR RESIDUE NH4 F 231
15BC6SOFTWARECL F:254 , HOH F:362BINDING SITE FOR RESIDUE NH4 F 236
16BC7SOFTWAREG38 C:110 , C42 F:223 , NH4 F:236BINDING SITE FOR RESIDUE CL F 254
17BC8SOFTWARECL F:253 , HOH F:359BINDING SITE FOR RESIDUE NH4 F 233
18BC9SOFTWAREA43 C:106 , NYM F:219 , NH4 F:233BINDING SITE FOR RESIDUE CL F 253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 363D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 363D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 363D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 363D)

(-) Exons   (0, 0)

(no "Exon" information available for 363D)

(-) 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:DNA  Length:12
                                            
                 363d A   1 cgcgaaxxcgcG  12
                            ||||||||10| 
                            ||||||||9-C42
                            1-C42|||10-G38
                             2-G38|| 11-C42
                              3-C42|    
                               4-G38    
                                5-A43   
                                 6-A43  
                                  7-NYM 
                                   8-NYM


Chain B from PDB  Type:DNA  Length:12
                                            
                 363d B  13 cgcgaaxxcgcG  24
                            ||||||||22| 
                            |||||||21-C42
                           13-C42|||22-G38
                            14-G38|| 23-C42
                             15-C42|    
                              16-G38    
                               17-A43   
                                18-A43  
                                 19-NYM 
                                  20-NYM


Chain C from PDB  Type:DNA  Length:12
                                            
                 363d C 101 cgcgaaxxcgcG 112
                            |||||||110| 
                            ||||||109-C42
                          101-C42||110-G38
                           102-G38||111-C42
                            103-C42|    
                             104-G38    
                              105-A43   
                               106-A43  
                                107-NYM 
                                 108-NYM


Chain D from PDB  Type:DNA  Length:12
                                            
                 363d D 113 cgcgaaxxcgcG 124
                            |||||||122| 
                            ||||||121-C42
                          113-C42||122-G38
                           114-G38||123-C42
                            115-C42|    
                             116-G38    
                              117-A43   
                               118-A43  
                                119-NYM 
                                 120-NYM


Chain E from PDB  Type:DNA  Length:12
                                            
                 363d E 201 cgcgaaxxcgcG 212
                            |||||||210| 
                            ||||||209-C42
                          201-C42||210-G38
                           202-G38||211-C42
                            203-C42|    
                             204-G38    
                              205-A43   
                               206-A43  
                                207-NYM 
                                 208-NYM


Chain F from PDB  Type:DNA  Length:12
                                            
                 363d F 213 cgcgaaxxcgcG 224
                            |||||||222| 
                            ||||||221-C42
                          213-C42||222-G38
                           214-G38||223-C42
                            215-C42|    
                             216-G38    
                              217-A43   
                               218-A43  
                                219-NYM 
                                 220-NYM
   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 363D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 363D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 363D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 363D)

 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
    A43  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    C42  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    G38  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NYM  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 363d)
 
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)
Insightii
  dinucleotide step, sticks
[ mono GIF format | stereo GIF format ]
  dinucleotide step, spacefill
[ mono GIF format | stereo GIF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  363d
    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 | HSSP
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 363D)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 363D)