Structure of PDB 6bkf Chain A

Receptor sequence

>6bkfA (length=562) Species: 9606 (Homo sapiens)

TVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKDVT
DSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLN
YRDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSL
LQLITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDL
EKVCRQLHDPSVGLSDISITLFSAFKPMLAAIADIEHIEKDMKHQSFYIE
TKLDGERMQMHKDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKA
DIQICILDGEMMAYNPNTQTFMQLQTCYCVFDVLMVNNKKLGHETLRKRY
EILSSIFTPIPGRIEIVQKTQAHTKNEVIDALNEAIDKREEGIMVKQPLS
IYKPDKRGEGWLKIKPEYVSGLMDELDILIVGGYWGKRGGMMSHFLCAVA
EKPPKPSVFHTLSRVGSGCTMKELYDLGLKLAKYWKPFHRKAPPSSILCG
TEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLRFPRIEKIRDDKEWH
ECMTLDDLEQLR

3D structure

• PDB: 6bkf Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis.
• Chain: A
• Resolution: 3.25 Å

Enzymatic activity

• Enzyme Commision number: 6.5.1.1: DNA ligase (ATP).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	Y82 G83 I84 K85 T87 M88 R278 S292 N294 Y296 Y298	Y71 G72 I73 K74 T76 M77 R257 S271 N273 Y275 Y277
BS02	dna	A	R293 R443 K449 K451	R272 R407 K413 K415
BS03	AMP	A	K273 L274 R278 F367 M430 K432 K449 K451	K252 L253 R257 F331 M394 K396 K413 K415

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003909 DNA ligase activity
• GO:0003910 DNA ligase (ATP) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006281 DNA repair
• GO:0006310 DNA recombination
• GO:0051103 DNA ligation involved in DNA repair
• GO:0071897 DNA biosynthetic process

External links

• PDB: RCSB:6bkf, PDBe:6bkf, PDBj:6bkf
• PDBsum: 6bkf
• PubMed: 29980672
• UniProt: P49917|DNLI4_HUMAN DNA ligase 4 (Gene Name=LIG4)