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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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.