Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 82170.98 
• Atom Count: 5417 
• Residue Count: 658 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

6BKG

Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation

• DOI: 10.2210/pdb6BKG/pdb

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


• Deposited: 2017-11-08 Released: 2018-07-18 
• Deposition Author(s): Moon, A.F., Tumbale, P.P., Schellenberg, M.J., Williams, R.S., Williams, J.G., Kunkel, T.A., Pedersen, L.C., Bebenek, B.
• Funding Organization(s): National Institutes of Health 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.402 Å
• R-Value Free: 0.245 
• R-Value Work: 0.201 

Literature

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., Williams, R.S., Williams, J.G., Kunkel, T.A., Pedersen, L.C., Bebenek, K.

(2018) Nat Commun 9: 2642-2642

• PubMed: 29980672 
• Primary Citation of Related Structures:  
  6BKF

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA ligase 4	A	621	Homo sapiens	Mutation(s): 0  Gene Names: LIG4 EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens) Go to Gene View: LIG4 Go to UniProtKB:  P49917

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

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	T	18	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3')	D	8	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AMP	D	NON-POLYMER	C10 H14 N5 O7 P		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.402 Å
• R-Value Free: 0.245 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 72.657	α = 90.00
b = 102.747	β = 90.00
c = 110.131	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-11-08 
• Released Date: 2018-07-18 
• Deposition Author(s): Moon, A.F., Tumbale, P.P., Schellenberg, M.J., Williams, R.S., Williams, J.G., Kunkel, T.A., Pedersen, L.C., Bebenek, B.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	1ZIA ES 102645
National Institutes of Health	United States	Z01 ES065070
National Institutes of Health	United States	1Z01 ES102765
National Institutes of Health	United States	ZES102488-09

Revision History 

• Version 1.0: 2018-07-18
  Type: Initial release