8PVW | pdb_00008pvw

Structure of a short E. coli adenylate kinase in complex with Ap5A

PDB DOI: https://doi.org/10.2210/pdb8PVW/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-07-18 Released: 2025-02-05
Deposition Author(s): Rodriguez, J.A., Wolf Watz, M., Sauer-Eriksson, E.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.234 (Depositor), 0.242 (DCC)
R-Value Work:
0.183 (Depositor), 0.192 (DCC)
R-Value Observed:
0.186 (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

Structure of a short E. coli adenylate kinase in complex with Ap5A

Rodriguez, J.A., Wolf Watz, M., Nagy, T.M., Phoeurk, C., Rogne, P., Schierholz, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 21.46 kDa
Atom Count: 1,616
Modeled Residue Count: 187
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A	187	Escherichia coli K-12	Mutation(s): 0 Gene Names: adk, dnaW, plsA, b0474, JW0463 EC: 2.7.4.3
UniProt
Find proteins for P69441 (Escherichia coli (strain K12)) Explore P69441 Go to UniProtKB: P69441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69441
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AP5 (Subject of Investigation/LOI) Query on AP5 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C₂₀ H₂₉ N₁₀ O₂₂ P₅ OIMACDRJUANHTJ-XPWFQUROSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.234 (Depositor), 0.242 (DCC)
R-Value Work: 0.183 (Depositor), 0.192 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.838	α = 90
b = 73.244	β = 90
c = 90.357	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-05

Deposition Author(s):

Rodriguez, J.A.

Sauer-Eriksson, E.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2021-04513_VR

Revision History (Full details and data files)

Version 1.0: 2025-02-05
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.