4JZK | pdb_00004jzk

Crystal Structure of Adenylate kinase of E. Coli with ADP/AMP bound

PDB DOI: https://doi.org/10.2210/pdb4JZK/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli O104:H4 str. 2009EL-2071
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-03 Released: 2014-04-30
Deposition Author(s): Cho, Y.-J., Agafonov, R., Kern, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.252 (Depositor), 0.253 (DCC)
R-Value Work:
0.214 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Crystal structure of E. Coli Adenylate kinase with ADP and AMP bound

Cho, Y.-J., Agafonov, R., Kern, D.

To be published.

Macromolecule Content

Total Structure Weight: 48.79 kDa
Atom Count: 4,109
Modeled Residue Count: 428
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	214	Escherichia coli O104:H4 str. 2009EL-2071	Mutation(s): 0 Gene Names: adk, O3O_06175 EC: 2.7.4.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.252 (Depositor), 0.253 (DCC)
R-Value Work: 0.214 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.96	α = 90
b = 78.8	β = 90
c = 83.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.