6V5K | pdb_00006v5k

Crystal structure of human DNA polymerase eta complexed with N7-nitrogen half-mustard guanine (NHMG) and dCTP*

• PDB DOI: https://doi.org/10.2210/pdb6V5K/pdb
• NAKB: 6V5K

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-04 Released: 2020-12-09 
• Deposition Author(s): Jung, H., Lee, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.242 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human DNA polymerase eta complexed with N7-nitrogen half-mustard guanine (NHMG) and dCTP*

Jung, H., Lee, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.12 kDa 
• Atom Count: 3,777 
• Modeled Residue Count: 445 
• Deposited Residue Count: 452 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase eta	A	432	Homo sapiens	Mutation(s): 0  Gene Names: POLH, RAD30, RAD30A, XPV EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens) Explore Q9Y253  Go to UniProtKB:  Q9Y253
PHAROS:  Q9Y253 GTEx:  ENSG00000170734

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')	B [auth P]	8	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*T*(QRV)P*CP*TP*CP*AP*CP*AP*CP*T)-3')	C [auth T]	12	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0KX	D [auth A]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine C9 H17 N4 O12 P3 STYMTWKSQLVXJN-SHYZEUOFSA-N
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.242 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.911	α = 90
b = 98.911	β = 90
c = 82.138	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Jung, H., Lee, S.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description