3CFR | pdb_00003cfr

Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 2

PDB DOI: https://doi.org/10.2210/pdb3CFR/pdb
NAKB: 3CFR

Classification: Transferase/DNA
Organism(s): Escherichia phage RB69
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-03-04 Released: 2009-03-10
Deposition Author(s): Wang, J., Klimenko, D., Wang, M., Steitz, T.A., Konigsberg, W.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.266 (Depositor), 0.270 (DCC)
R-Value Work:
0.192 (Depositor), 0.202 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant

Klimenko, D., Wang, M., Steitz, T.A., Konigsberg, W.H., Wang, J.

To be published.

Macromolecule Content

Total Structure Weight: 115.6 kDa
Atom Count: 8,636
Modeled Residue Count: 932
Deposited Residue Count: 940
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	C [auth A]	909	N/A	Mutation(s): 3 Gene Names: 43 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for Q38087 (Escherichia phage RB69) Explore Q38087 Go to UniProtKB: Q38087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q38087
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(DTPDCPDAPDAPDGPDTPDAPDAPDGPDCPDAPDGPDTPDCPDCPDGPDCPDG)-3')	A [auth T]	18	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(DGPDCPDGPDGPDAPDCPDTPDGPDCPDTPDTPDAP*(DOC))-3')	B [auth P]	13	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TTP Query on TTP Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	THYMIDINE-5'-TRIPHOSPHATE C₁₀ H₁₇ N₂ O₁₄ P₃ NHVNXKFIZYSCEB-XLPZGREQSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]