6PSP | pdb_00006psp

Adenylate kinase from Methanococcus igneus - AP5A bound form

• PDB DOI: https://doi.org/10.2210/pdb6PSP/pdb

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


• Deposited: 2019-07-13 Released: 2020-07-01 
• Deposition Author(s): Moon, S., Kim, J., Bae, E., Phillips Jr., G.N.
• Funding Organization(s): National Research Foundation (NRF, Korea), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Adenylate kinase from Methanococcus igneus - AMP bound form

Bae, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 140.5 kDa 
• Atom Count: 9,307 
• Modeled Residue Count: 1,146 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C, D, E, F	200	Methanotorris igneus	Mutation(s): 0  Gene Names: adkA, adk EC: 2.7.4.3
UniProt
Find proteins for P43408 (Methanotorris igneus) Explore P43408  Go to UniProtKB:  P43408

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.443	α = 90
b = 122.627	β = 100.2
c = 83.721	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Moon, S., Kim, J., Bae, E., Phillips Jr., G.N.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	PJ013181
National Science Foundation (NSF, United States)	United States	1231306

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Structure summary
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Refinement description