6BKG

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase 4
A
621Homo sapiensMutation(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
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')P11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')T18synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3')D8synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AMP
Query on AMP
D
NON-POLYMERC10 H14 N5 O7 P

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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 = 72.657α = 90.00
b = 102.747β = 90.00
c = 110.131γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States1ZIA ES 102645
National Institutes of HealthUnited StatesZ01 ES065070
National Institutes of HealthUnited States1Z01 ES102765
National Institutes of HealthUnited StatesZES102488-09

Revision History 

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