9QPC | pdb_00009qpc

DNA polymerase with inhibitor

PDB DOI: https://doi.org/10.2210/pdb9QPC/pdb
EM Map EMD-53270: EMDB EMDataResource
NAKB: 9QPC

Classification: DNA BINDING PROTEIN
Organism(s): Enterococcus faecium, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-03-26 Released: 2025-09-24
Deposition Author(s): Lamers, M.H., Urem, M., Smits, W.K.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

DNA polymerase with inhibitor

Lamers, M.H., Urem, M., Smits, W.K.

To be published.

Macromolecule Content

Total Structure Weight: 191.08 kDa
Atom Count: 10,165
Modeled Residue Count: 1,240
Deposited Residue Count: 1,552
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III PolC-type	A	1,474	Enterococcus faecium	Mutation(s): 2 Gene Names: polC, CI258_000840 EC: 2.7.7.7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPAP*A)-3')	B [auth E]	3	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPAPGPGPTPGPCPGPCPAP*T)-3')	C [auth P]	33	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PCPCPAPTPGPCPGPCPAPCPCPTP*A)-3')	D [auth T]	42	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I88 Query on A1I88 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-[[2,2-bis(fluoranyl)-1,3-benzodioxol-5-yl]methylamino]-3-fluoranyl-1-(2-hydroxyethyl)-6~{H}-pyrazolo[4,3-d]pyrimidin-7-one C₁₅ H₁₂ F₃ N₅ O₄ KHEIVJSMPVGALA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]