3GDX

Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP

PDB DOI: https://doi.org/10.2210/pdb3GDX/pdb
NAKB: 3GDX

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

Deposited: 2009-02-24 Released: 2009-05-05
Deposition Author(s): Wilson, S.H., Batra, V.K., Pedersen, L.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.266 (Depositor), 0.250 (DCC)
R-Value Work:
0.208 (Depositor), 0.190 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function

Upton, T.G., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Prakash, G.K., Kultyshev, R., Batra, V.K., Shock, D.D., Pedersen, L.C., Beard, W.A., Wilson, S.H.

(2009) Org Lett 11: 1883-1886

PubMed: 19351147 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ol701755k
Primary Citation of Related Structures:
3GDX

PubMed Abstract:
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.

Organizational Affiliation

Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.

Macromolecule Content

Total Structure Weight: 47.31 kDa
Atom Count: 3,601
Modelled Residue Count: 357
Deposited Residue Count: 357
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	326	Homo sapiens	Mutation(s): 0 Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746 Go to UniProtKB: P06746
PHAROS: P06746 GTEx: ENSG00000070501
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06746
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(CPCPGPAPCPAPGPCPGPCPAPTPCPAPGPC)-3'	B [auth T]	16	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(GPCPTPGPAPTPGPCPGPC)-3'	C [auth P]	10	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(PGPTPCPGP*G)-3'	D	5	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4BD Query on 4BD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine C₁₁ H₁₇ F₂ N₂ O₁₃ P₃ WQZXQECPJNOPSV-XLPZGREQSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.266 (Depositor), 0.250 (DCC)
R-Value Work: 0.208 (Depositor), 0.190 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.5	α = 90
b = 79.7	β = 107.9
c = 55.3	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

Wilson, S.H.

Batra, V.K.

Pedersen, L.C.

Revision History (Full details and data files)

Version 1.0: 2009-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description