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
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)

(-) Description

Title :  PURINE 2'-DEOXYRIBOSYL COMPLEX WITH ARABINOSIDE: RIBOSYLATED INTERMEDIATE (ARAA)
 
Authors :  R. Anand, P. A. Kaminski, S. E. Ealick
Date :  08 Jan 04  (Deposition) - 30 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Ribosylate Intermediate, Ptd, Araa, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Anand, P. A. Kaminski, S. E. Ealick
Structures Of Purine 2'-Deoxyribosyltransferase, Substrate Complexes, And The Ribosylated Enzyme Intermediate At 2. 0 A Resolution.
Biochemistry V. 43 2384 2004
PubMed-ID: 14992575  |  Reference-DOI: 10.1021/BI035723K

(-) Compounds

Molecule 1 - PURINE TRANS DEOXYRIBOSYLASE
    Chains: A, B, C
    EC Number: 2.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PURINE 2'-DEOXYRIBOSYLTRANSFERASE
    Organism Scientific: LACTOBACILLUS HELVETICUS
    Organism Taxid: 1587

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ADE3Ligand/IonADENINE
2AR43Mod. Amino Acid2-AMINO-5-(3-FLUORO-3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-5-HYDROXY-PENTANOIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ADE6Ligand/IonADENINE
2AR46Mod. Amino Acid2-AMINO-5-(3-FLUORO-3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-5-HYDROXY-PENTANOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:44 , PHE A:45 , THR A:71 , ASP A:75 , AR4 A:101 , TYR C:167BINDING SITE FOR RESIDUE ADE A 1245
2AC2SOFTWAREPRO B:44 , THR B:71 , ASP B:75 , AR4 B:101 , TYR B:167 , HOH B:1269 , HOH B:1329 , HOH B:1333BINDING SITE FOR RESIDUE ADE B 1246
3AC3SOFTWAREPRO C:44 , PHE C:45 , THR C:71 , ASP C:75 , AR4 C:101 , HOH C:1293 , HOH C:1317 , HOH C:1333BINDING SITE FOR RESIDUE ADE C 1247

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S2D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S2D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S2D)

(-) Exons   (0, 0)

(no "Exon" information available for 1S2D)

(-) 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:165
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2da_ A: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2dA00 A:1-167  [code=3.40.50.1810, no name d efined]                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhh....eeeee....-........-.......hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eehhhhhhhh.ee.....hhhhhhh..............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2d A   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFD-GFTDPDEK-PEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFeIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40     | |50    | | 60        70        80        90       100|      110       120       130       140       150       160       
                                                                        46 |     55 |                                         101-AR4                                                              
                                                                          48       57                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2db_ B: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2dB00 B:1-167  [code=3.40.50.1810, no name defined]                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.hhhhhhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2d B   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFeIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100|      110       120       130       140       150       160       
                                                                                                                              101-AR4                                                              


Chain C from PDB  Type:PROTEIN  Length:167
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2dc_ C: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2dC00 C:1-167  [code=3.40.50.1810, no name defined]                                                                                                                   CATH domains
           Pfam domains (1) ---------Nuc_deoxyrib_tr-1s2dC01 C:10-130                                                                                         ------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Nuc_deoxyrib_tr-1s2dC02 C:10-130                                                                                         ------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------Nuc_deoxyrib_tr-1s2dC03 C:10-130                                                                                         ------------------------------------- Pfam domains (3)
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.hhhhhhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2d C   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFeIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100|      110       120       130       140       150       160       
                                                                                                                              101-AR4
   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, 3)

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

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Nribosyltransf (19)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8RLY5_LACHE | Q8RLY5)
molecular function
    GO:0070694    deoxyribonucleoside 5'-monophosphate N-glycosidase activity    Catalysis of the reaction: a deoxyribonucleoside 5'-monophosphate + H2O = deoxyribose 5-monophosphate + a purine or pyrimidine base.
    GO:0050144    nucleoside deoxyribosyltransferase activity    Catalysis of the reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009159    deoxyribonucleoside monophosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.

 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
    ADE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AR4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s2d)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1s2d
    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
  Q8RLY5_LACHE | Q8RLY5
    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)
  2.4.2.6
    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
  Q8RLY5_LACHE | Q8RLY5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8RLY5_LACHE | Q8RLY5: 1s2g 1s2i 1s2l 1s3f

(-) Related Entries Specified in the PDB File

1f8y STRUCTURE OF 2'-DEOXYRIBOSYLTRANSFERASE(NTD)
1s2g PURINE 2'DEOXYRIBOSYLTRANSFERASE + 2'-DEOXYADENOSINE
1s2i PURINE 2'DEOXYRIBOSYLTRANSFERASE + BROMOPURINE
1s2l PURINE 2'DEOXYRIBOSYLTRANSFERASE NATIVE STRUCTURE
1s3f PURINE 2'-DEOXYRIBOSYLTRANSFERASE + SELENOINOSINE