8W1M | pdb_00008w1m

T.thermophilus DNAK nucleotide binding domain in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb8W1M/pdb

Classification: CHAPERONE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-16 Released: 2025-02-26
Deposition Author(s): Miller, D.J., Kalodimos, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.259 (Depositor), 0.235 (DCC)
R-Value Work:
0.225 (Depositor), 0.226 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

T.thermophilus DNAK nucleotide binding domain in complex with ADP

Miller, D.J., Kalodimos, C.

To be published.

Macromolecule Content

Total Structure Weight: 83.62 kDa
Atom Count: 5,779
Modeled Residue Count: 760
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK	A, B	382	Thermus thermophilus	Mutation(s): 0 Gene Names: dnaK, TTHA1491
UniProt
Find proteins for Q56235 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q56235 Go to UniProtKB: Q56235
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q56235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]