› 4k4i

X-ray diffraction
2.25Å resolution

Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP.

Released:
DOI: 10.2210/pdb4k4i/pdb
PDB entry 4k4i coloured by chain, front view.
PDB entry 4k4i coloured by chain, side view.
PDB entry 4k4i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase λ.
Vyas R, Zahurancik WJ, Suo Z
Proc Natl Acad Sci U S A 111 E3033-42 (2014)
PMID: 25015085

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117721 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase lambda Chains: A, E, I, M
Molecule details ›
Chains: A, E, I, M
Length: 340 amino acids
Theoretical weight: 38.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UGP5 (Residues: 245-575; Coverage: 58%)
Gene name: POLL
Sequence domains:
Structure domains:
DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3') Chains: B, F, J, N
Molecule details ›
Chains: B, F, J, N
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') Chains: C, G, K, O
Molecule details ›
Chains: C, G, K, O
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*CP*CP*G)-3') Chains: D, H, L, P
Molecule details ›
Chains: D, H, L, P
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand 1RY 4 x 1RY
Ligand CA 23 x CA
Ligand ACT 6 x ACT
Ligand CAC 2 x CAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21212
Unit cell:
a: 194.44Å b: 97.58Å c: 105.15Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.212 0.274
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 citation in other articles

Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine.
Bertoletti et al. (2019)
5 more

2 mentions without citation

Elucidating molecular interactions of L-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance.
Hung et al. (2019)
1 more