4K8Z

KOD Polymerase in binary complex with dsDNA

PDB DOI: https://doi.org/10.2210/pdb4K8Z/pdb
NAKB: 4K8Z

Classification: TRANSFERASE/DNA
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-04-19 Released: 2013-06-26
Deposition Author(s): Bergen, K., Betz, K., Welte, W., Diederichs, K., Marx, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 ?
R-Value Free: 0.218
R-Value Work: 0.181
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex

Bergen, K., Betz, K., Welte, W., Diederichs, K., Marx, A.

(2013) Chembiochem 14: 1058-1062

PubMed: 23733496 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201300175
Primary Citation of Related Structures:
4K8X, 4K8Z

PubMed Abstract:
Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.

Organizational Affiliation

Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universit?tsstrasse 10, 78457 Konstanz, Germany.

Macromolecule Content

Total Structure Weight: 98.92 kDa
Atom Count: 7,141
Modelled Residue Count: 782
Deposited Residue Count: 802
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	774	Thermococcus kodakarensis KOD1	Mutation(s): 2 Gene Names: pol, pol TK0001, TK0001 EC: 2.7.7.7
UniProt
Find proteins for P77933 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore P77933 Go to UniProtKB: P77933
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P77933
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

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

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPGPCPGPAPAPCPTPGPCPGP(2DA))-3')	C [auth P]	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth T] MOL2 format, chain G [auth T] mmCIF format, chain G [auth T]	G [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth T] Interactions & Density Focus chain G [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 ?
R-Value Free: 0.218
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 144.87	α = 90
b = 111.78	β = 90
c = 67.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2017-08-09
Changes: Refinement description, Source and taxonomy
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary