2ECK

STRUCTURE OF PHOSPHOTRANSFERASE

PDB DOI: https://doi.org/10.2210/pdb2ECK/pdb
Entry: 2ECK supersedes: 1ECK

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1996-12-16 Released: 1997-03-12
Deposition Author(s): Berry, M.B., Bilderback, T., Glaser, M., Phillips Jr., G.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.276
R-Value Work: 0.193
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase.

Berry, M.B., Bae, E., Bilderback, T.R., Glaser, M., Phillips, G.N.

(2006) Proteins 62: 555-556

PubMed: 16302237 Search on PubMed
DOI: https://doi.org/10.1002/prot.20699
Primary Citation of Related Structures:
2ECK

Organizational Affiliation

W. M. Keck Center for Computational Biology, Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA.

Macromolecule Content

Total Structure Weight: 48.79 kDa
Atom Count: 3,474
Modelled Residue Count: 428
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENYLATE KINASE	A, B	214	Escherichia coli	Mutation(s): 0 Gene Names: ADK+ 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 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]	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]
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]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.276
R-Value Work: 0.193
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.5	α = 90
b = 84.8	β = 90
c = 80.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1997-03-12

Deposition Author(s):

This entry supersedes: 1ECK

Revision History (Full details and data files)

Version 1.0: 1997-03-12
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-03-07
Changes: Data collection, Other
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

2ECK

STRUCTURE OF PHOSPHOTRANSFERASE

Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)