PDBsum entry 8v1v

Ligase/DNA

PDB id: 8v1v

Contents

Protein chain

645 a.a.

DNA/RNA

Ligands

GOL ×3

MES ×2

AMP

Metals

_NA

Waters ×239

PDB id:

8v1v

Name:

Ligase/DNA

Title:

Human DNA ligase i f872l bound to adenylated nicked DNA

Structure:

DNA ligase 1. Chain: a. Synonym: DNA ligase i,polydeoxyribonucleotide synthase [atp] 1. Engineered: yes. Mutation: yes. DNA (5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp Tp C)-3'). Chain: b. Engineered: yes. DNA (5'-d(p Gp Tp Cp Gp Gp Ap C)-3').

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: lig1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.30Å R-factor: 0.181 R-free: 0.223

Authors:

P.P.Tumbale,R.S.Williams

Key ref:

P.P.Tumbale and r.s.williams Human DNA ligase i f872l bound to adenylated nicked d. To be published, .

Date:

21-Nov-23 Release date: 02-Jul-25

Protein chain

P18858  (DNLI1_HUMAN) -  DNA ligase 1 from Homo sapiens

Seq: 919 a.a.

Struc: 645 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

G-C-T-G-A-T-G-C-G-T-C 11 bases

G-T-C-G-G-A-C 7 bases

G-T-C-C-G-A-OHU-G-A-C-G-C-A-T-C-A-G-C 18 bases

Enzyme reactions

• Enzyme class: E.C.6.5.1.1 - Dna ligase (ATP).
• Reaction: ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate

ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP (Bound ligand (Het Group name = AMP) corresponds exactly) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site