3VNN: DNA ligase 4

Name: PDB 3VNN: Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV
Published: 2012-06-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV. Determined by X-ray diffraction at 2.9 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 952
Mol. weight: 16.2 kDa
Released: 20 Jun 2012

Explore 3VNN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VNN contains 2 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	277-284	8	1
β-strand	287-291	5	1
β-strand	297	1	1
α-helix	314-316	3
β-strand	325-336	12	1
β-strand	341-342	2	1
β-strand	361-365	5	1
β-strand	366	1	2
β-strand	367-372	6	1
β-strand	375-376	2	1
α-helix	382-392	11
β-strand	396	1	3
β-strand	399	1	3
β-strand	402	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA ligase 4	A	protein	139	Homo sapiens	P49917 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VNN_1 DNA ligase 4 (chains A)
FYIETKLDGERMQMHKDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICI
LDGEMMAYNPNTQTFMQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYE
ILSSIFTPIPGRIEIVQKT

Primary citation

Structural insights into the role of domain flexibility in human DNA ligase IV. Ochi, T., Wu, Q., Chirgadze, D.Y. et al. Structure (2012) 20:1212-1222. DOI 10.1016/j.str.2012.04.012 · PubMed

Other PDB entries of the same protein (UniProt P49917 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HTP 2.25 Å, Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide
1IK9 2.3 Å, Crystal structure of a XRCC4-DNA ligase IV complex
3II6 2.4 Å, Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.
3W1B 2.4 Å, Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative)
6BKG 2.4 Å, Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation
3W1G 2.55 Å, Crystal Structure of Human DNA ligase IV-Artemis Complex (Native)
7D9Y 2.76 Å, DNA binding domain of human DNA Ligase IV mutant - A3V
9CQ3 2.8 Å, The gap-filling complex with Pol mu engaged in the NHEJ pathway
9N81 2.8 Å, A gap-filling complex with Pol mu engaged in the NHEJ Pathway
4HTO 2.81 Å, Crystal structure of the DBD domain of human DNA ligase IV Apo form
3W5O 2.84 Å, Crystal Structure of Human DNA ligase IV
7D9K 2.9 Å, DNA binding domain of human DNA Ligase IV - Wild type

Browse structure collections

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