› 4ph5

X-ray diffraction
2.55Å resolution

Structure of human DNA polymerase beta complexed with a nicked DNA containing a AC at N-1 position and GC at N position

Released:
DOI: 10.2210/pdb4ph5/pdb
PDB entry 4ph5 coloured by chain, front view.
PDB entry 4ph5 coloured by chain, side view.
PDB entry 4ph5 coloured by chain, top view.
Source organisms:
Entry authors: Koag MC, Lee S

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117974 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 326 amino acids
Theoretical weight: 37.18 KDa
Source organism: Homo sapiens
Expression system: Enterobacteria phage L1
UniProt:
  • Canonical: P06746 (Residues: 10-335; Coverage: 97%)
Gene name: POLB
Sequence domains:
Structure domains:
DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.85 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*CP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 50.613Å b: 80.377Å c: 55.294Å
α: 90° β: 107.61° γ: 90°
R-values:
R R work R free
0.194 0.191 0.261
Expression systems:
  • Enterobacteria phage L1
  • Not provided

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