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 :  DNA POLYMERASE BETA OPEN PRODUCT COMPLEX WITH 8-OXOG:C AND INSERTED DCTP
 
Authors :  B. D. Freudenthal, M. R. Smith, A. M. Whitaker, M. A. Schaich
Date :  02 Mar 17  (Deposition) - 10 May 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Transferase Ligase / Dna, Transferase-Dna, Ligase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Whitaker, M. R. Smith, M. A. Schaich, B. D. Freudenthal
Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide.
Nucleic Acids Res. 2017
PubMed-ID: 28449123  |  Reference-DOI: 10.1093/NAR/GKX293

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA
    Chains: A
    EC Number: 2.7.7.7, 4.2.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POLB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3')
    Chains: T
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*GP*TP*CP*GP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:101 , VAL A:103 , ILE A:106 , HOH A:517 , DG P:9 , HOH P:101binding site for residue NA A 401
2AC2SOFTWARELYS A:60 , LEU A:62 , VAL A:65 , DC D:3 , HOH D:102binding site for residue NA A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V1J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:274 -Ser A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V1J)

(-) Exons   (0, 0)

(no "Exon" information available for 5V1J)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeee........ee..eeeeee..............hhhhhhhhhhh..eeeeeee...eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..............hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v1j A  13 GGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE 335
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242||     256       266       276       286       296       306       316       326         
                                                                                                                                                                                                                                                                243|                                                                                       
                                                                                                                                                                                                                                                                 248                                                                                       


Chain D from PDB  Type:DNA  Length:5
                                     
                 5v1j D   1 GTCGG   5


Chain P from PDB  Type:DNA  Length:11
                                           
                 5v1j P   1 GCTGATGCGxC  11
                                    10 
                                    10-8OG


Chain T from PDB  Type:DNA  Length:16
                                                
                 5v1j T   1 CCGACGCCGCATCAGC  16
                                    10
   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 5V1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V1J)

(-) Gene Ontology  (44, 44)

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
    8OG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:274 - Ser A:275   [ 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
  5v1j
    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
  DPOLB_HUMAN | P06746
    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)
  2.7.7.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  4.2.99.-
    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
  DPOLB_HUMAN | P06746
    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
        DPOLB_HUMAN | P06746: 1bpx 1bpy 1bpz 1mq2 1mq3 1tv9 1tva 1zjm 1zjn 1zqa 1zqb 1zqc 1zqd 1zqe 1zqf 1zqg 1zqh 1zqi 1zqj 1zqk 1zql 1zqm 1zqn 1zqo 1zqp 1zqq 1zqr 1zqs 1zqt 2fmp 2fmq 2fms 2i9g 2iso 2isp 2p66 2pxi 3c2k 3c2l 3c2m 3gdx 3isb 3isc 3isd 3jpn 3jpo 3jpp 3jpq 3jpr 3jps 3jpt 3lk9 3mby 3ogu 3rh4 3rh5 3rh6 3rje 3rjf 3rjg 3rjh 3rji 3rjj 3rjk 3tfr 3tfs 4do9 4doa 4dob 4doc 4f5n 4f5o 4f5p 4f5q 4f5r 4gxi 4gxj 4gxk 4jwm 4jwn 4kld 4kle 4klf 4klg 4klh 4kli 4klj 4kll 4klm 4klo 4klq 4kls 4klt 4klu 4lvs 4m2y 4m47 4m9g 4m9h 4m9j 4m9l 4m9n 4mf2 4mf8 4mfa 4mfc 4mff 4nlk 4nln 4nlz 4nm1 4nm2 4nxz 4ny8 4o5c 4o5e 4o5k 4o9m 4p2h 4pgq 4pgx 4pgy 4ph5 4pha 4phd 4phe 4php 4ppx 4r63 4r64 4r65 4r66 4rpx 4rpy 4rpz 4rq0 4rq1 4rq2 4rq3 4rq4 4rq5 4rq6 4rq7 4rq8 4rt2 4rt3 4tup 4tuq 4tur 4tus 4uaw 4uay 4uaz 4ub1 4ub2 4ub3 4ub4 4ub5 4ubb 4ubc 4ymm 4ymn 4ymo 4yn4 4z6c 4z6d 4z6e 4z6f 5bol 5bom 5bpc 5db6 5db7 5db8 5db9 5dba 5dbb 5dbc 5eoz 5hhh 5hhi 5j0o 5j0p 5j0q 5j0r 5j0s 5j0t 5j0u 5j0w 5j0x 5j0y 5j29 5j2a 5j2b 5j2c 5j2d 5j2e 5j2f 5j2g 5j2h 5j2i 5j2j 5j2k 5tb8 5tb9 5tba 5tbb 5tbc 5tzv 5u2r 5u2s 5u2t 5u8g 5u8h 5u8i 5u9h 5v1f 5v1g 5v1h 5v1i 5v1n 5v1o 5v1p 5v1r 5vez 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8ica 8icb 8icc 8ice 8icf 8icg 8ich 8ici 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 8icz 9ica 9icb 9icc 9ice 9icf 9icg 9ich 9ici 9icj 9ick 9icl 9icm 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv 9icw 9icx 9icy

(-) Related Entries Specified in the PDB File

5vif 5vig 5vih 5vii 5vin 5vio 5vip 5vir