8V1U | pdb_00008v1u

Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide

• PDB DOI: https://doi.org/10.2210/pdb8V1U/pdb
• NAKB: 8V1U

• Classification: LIGASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-21 Released: 2025-07-02 
• Deposition Author(s): Tumbale, P.P., Williams, R.S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide

Tumbale, P.P., Williams, R.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 83.98 kDa 
• Atom Count: 6,210 
• Modeled Residue Count: 680 
• Deposited Residue Count: 683 
• Unique protein chains: 1
• Unique nucleic acid chains: 2
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase 1	A	647	Homo sapiens	Mutation(s): 1  Gene Names: LIG1 EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P18858 (Homo sapiens) Explore P18858  Go to UniProtKB:  P18858
PHAROS:  P18858 GTEx:  ENSG00000105486

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')	B	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')	C	7	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	D	18	synthetic construct

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	K [auth C]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MES (Subject of Investigation/LOI)	F [auth A], G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	J [auth B], L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.986	α = 90
b = 96.832	β = 90
c = 114.661	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Tumbale, P.P., Williams, R.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1Z01ES102765

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release