4IKE | pdb_00004ike

Crystal Structure of a partly open ATP-lid of liganded Adenylate kinase

PDB DOI: https://doi.org/10.2210/pdb4IKE/pdb

Classification: TRANSFERASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-26 Released: 2014-07-02
Deposition Author(s): Cho, Y.-J., Kern, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.161 (Depositor), 0.164 (DCC)
R-Value Observed:
0.163 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The ATP-Lid Opened Adenylate Kinase with Fully Occupied Substrates

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

To be published.

Macromolecule Content

Total Structure Weight: 48.09 kDa
Atom Count: 4,060
Modeled Residue Count: 412
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	206	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: adk, Aquifex, aq_078 EC: 2.7.4.3
UniProt
Find proteins for O66490 (Aquifex aeolicus (strain VF5)) Explore O66490 Go to UniProtKB: O66490
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66490
Sequence Annotations Expand
Reference Sequence

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 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-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-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]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.198 (Depositor), 0.200 (DCC)
R-Value Work: 0.161 (Depositor), 0.164 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.37	α = 90
b = 61.57	β = 94.33
c = 58.89	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
AutoBuild	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
AutoBuild	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-02
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.