7D9Y: DNA ligase 4

Name: PDB 7D9Y: DNA binding domain of human DNA Ligase IV mutant - A3V
Published: 2021-02-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

DNA binding domain of human DNA Ligase IV mutant - A3V. Determined by X-ray diffraction at 2.76 Å resolution. Released 24 Feb 2021.

Method: X-ray diffraction
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,737
Mol. weight: 27.66 kDa
Released: 24 Feb 2021

Explore 7D9Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D9Y contains 14 α-helices and 4 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: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	1
α-helix	10-12	3
β-strand	15	1	2
α-helix	16-28	13
α-helix	32-55	24
β-strand	61	1	1
α-helix	65-71	7
α-helix	73-75	3
α-helix	86-96	11
α-helix	99-100	2
α-helix	104-110	7
α-helix	125-133	9
β-strand	144	1	2
α-helix	145-160	16
α-helix	164-176	13
α-helix	180-191	12
α-helix	200-214	15
α-helix	221-229	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA ligase 4	A	protein	243	Homo sapiens	P49917 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7D9Y_1 DNA ligase 4 (chains A)
GSHMAVSQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNH
KDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTG
THGDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQ
SSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSD
ISI

Primary citation

Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability. Maddi, E.R., Raghavan, S.C., Natesh, R. Protein Eng Des Sel (2021) 34. DOI 10.1093/protein/gzab001 · 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)
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
3VNN 2.9 Å, Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of…

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