3W5O: Human DNA ligase IV

Name: PDB 3W5O: Crystal Structure of Human DNA ligase IV
Published: 2013-04-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal Structure of Human DNA ligase IV. Determined by X-ray diffraction at 2.84 Å resolution. Released 3 Apr 2013.

Method: X-ray diffraction
Resolution: 2.84 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,003
Mol. weight: 142.4 kDa
Ligands: ATP
Released: 3 Apr 2013

Explore 3W5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3W5O contains 67 α-helices and 58 β-strands across 2 chains. 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: 32 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-27	12
α-helix	32-53	22
α-helix	65-71	7
α-helix	73-75	3
α-helix	86-97	12
α-helix	104-110	7
α-helix	125-133	9
α-helix	139-141	3
β-strand	144	1	1
α-helix	145-160	16
α-helix	164-176	13
α-helix	180-191	12
α-helix	200-207	8
α-helix	211-215	5
α-helix	221-227	7
α-helix	246-249	4
β-strand	250-253	4	2
α-helix	256-258	3
α-helix	259-262	4
β-strand	268-273	6	2
β-strand	277-284	8	3
β-strand	287-292	6	3
β-strand	297	1	3
α-helix	299-302	4
α-helix	312-315	4
α-helix	316-318	3
β-strand	319	1	4
β-strand	325-336	12	3
β-strand	341-343	3	3
α-helix	344	1
α-helix	351-356	6
β-strand	361-372	12	3
β-strand	375-376	2	3
α-helix	382-389	8
β-strand	393	1	4
β-strand	396	1	3
β-strand	400-402	3	3
α-helix	403-404	2
β-strand	405-408	4	2
α-helix	411-423	13
β-strand	428-432	5	2
α-helix	436-438	3
β-strand	443-450	8	2
β-strand	462-470	9	5
β-strand	482-488	7	5
α-helix	489-492	4
β-strand	500-507	8	5
α-helix	513-522	10
α-helix	523-525	3
β-strand	527-528	2	5
β-strand	538-539	2	5
β-strand	547-548	2	5
α-helix	551-553	3
β-strand	556-560	5	5
β-strand	563-566	4	6
β-strand	574-577	4	6
β-strand	580-585	6	5
α-helix	590-592	3
β-strand	595	1	5
α-helix	596-602	7

Chain B: 35 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	15	1	7
α-helix	16-27	12
α-helix	32-53	22
α-helix	65-71	7
α-helix	73-75	3
α-helix	86-97	12
α-helix	104-110	7
α-helix	125-133	9
α-helix	139-141	3
β-strand	144	1	7
α-helix	145-160	16
α-helix	164-176	13
α-helix	180-191	12
α-helix	200-207	8
α-helix	211-215	5
α-helix	221-227	7
α-helix	234-235	2
α-helix	246-249	4
β-strand	250-253	4	8
α-helix	256-258	3
α-helix	259-262	4
β-strand	268-272	5	8
β-strand	277-284	8	9
β-strand	287-292	6	9
β-strand	297	1	9
α-helix	299-302	4
α-helix	312-315	4
α-helix	316-318	3
β-strand	319	1	10
β-strand	325-336	12	9
β-strand	341-343	3	9
α-helix	344	1
α-helix	351-356	6
β-strand	361-372	12	9
β-strand	375-376	2	9
α-helix	382-389	8
β-strand	393	1	10
β-strand	396	1	9
β-strand	400-402	3	9
α-helix	403-404	2
β-strand	405-408	4	8
α-helix	411-423	13
β-strand	429-432	4	8
α-helix	436-438	3
β-strand	443-450	8	8
β-strand	462-471	10	11
β-strand	480-488	9	11
α-helix	489-492	4
α-helix	496-497	2
β-strand	500-507	8	11
α-helix	513-522	10
α-helix	523-525	3
β-strand	527-528	2	11
β-strand	538-539	2	11
β-strand	547-548	2	11
α-helix	551-553	3
β-strand	556-560	5	11
β-strand	563-566	4	12
β-strand	574-577	4	12
β-strand	580-585	6	11
α-helix	590-592	3
β-strand	595	1	11
α-helix	596-602	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA ligase 4	A, B	protein	610	Homo sapiens	P49917 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3W5O_1 DNA ligase 4 (chains A, B)
TMAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKD
VTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTH
GDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSS
ALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDIS
ITLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYNYT
DQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVEDSD
LQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDALN
EAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKGSRGGM
MSHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSSIL
CGTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWHECMTLDDL
EQLRGKASGK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair. Ochi, T., Gu, X., Blundell, T.L. Structure (2013) 21:672-679. DOI 10.1016/j.str.2013.02.014 · 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
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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