6BKF: DNA ligase 4

Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation. Determined by X-ray diffraction at 3.25 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,861
Mol. weight: 82.03 kDa
Ligands: AMP
Released: 18 Jul 2018

Explore 6BKF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BKF contains 28 α-helices and 29 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: 28 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	16-28	13
α-helix	32-54	23
α-helix	65-71	7
α-helix	73-75	3
α-helix	86-97	12
α-helix	104-110	7
α-helix	125-136	12
β-strand	144	1	1
α-helix	145-160	16
α-helix	164-176	13
α-helix	180-190	11
α-helix	200-207	8
α-helix	211-216	6
α-helix	221-227	7
α-helix	247-249	3
β-strand	252-253	2	2
α-helix	254	1
α-helix	256-258	3
α-helix	259-262	4
β-strand	268-272	5	2
β-strand	277-284	8	3
β-strand	287-291	5	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	341-342	2	3
β-strand	361-372	12	3
β-strand	375-376	2	3
α-helix	382-392	11
β-strand	393	1	4
β-strand	396	1	3
β-strand	400-402	3	3
β-strand	405-408	4	2
α-helix	411-423	13
β-strand	429-432	4	2
β-strand	447-450	4	2
α-helix	458-460	3
β-strand	462-471	10	5
β-strand	480-488	9	5
β-strand	500-507	8	5
α-helix	513-521	9
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	580-584	5	5
α-helix	590-592	3
β-strand	595	1	5
α-helix	596-602	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA ligase 4	A	protein	621	Homo sapiens	P49917 (AlphaFold model)
DNA (5'-d(gpcptpgpaptpgpcpgptp*c)-3')	P	DNA	11	synthetic construct
DNA (5'-d(gptpcpcpgpapcpgpapcpgpcpaptpcpapgpc)-3')	T	DNA	18	synthetic construct
DNA (5'-d(pgptpcpgpgpap*c)-3')	D	DNA	7	synthetic construct

Sequence of entity 1 (A), FASTA

>6BKF_1 DNA ligase 4 (chains A)
TMAASQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKD
VTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTH
GDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSS
ALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDIS
ITLFSAFKPMLAAIADIEHIEKDMKHQSFYIETKLDGERMQMHKDGDVYKYFSRNGYNYT
DQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRMVEDSD
LQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEIVQKTQAHTKNEVIDALN
EAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKGSRGGM
MSHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSSIL
CGTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWHECMTLDDL
EQLRGKASGKLASKHLYIGGD

Sequence of entity 2 (P), FASTA

>6BKF_2 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3') (chains P)
GCTGATGCGTC

Sequence of entity 3 (T), FASTA

>6BKF_3 DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') (chains T)
GTCCGACGACGCATCAGC

Sequence of entity 4 (D), FASTA

>6BKF_4 DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') (chains D)
GTCGGAC

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1

Primary citation

Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis. Kaminski, A.M., Tumbale, P.P., Schellenberg, M.J. et al. Nat Commun (2018) 9:2642-2642. DOI 10.1038/s41467-018-05024-8 · 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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