5YT3 | pdb_00005yt3

Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 S218D and S222D mutant

• PDB DOI: https://doi.org/10.2210/pdb5YT3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-11-16 Released: 2018-11-21 
• Deposition Author(s): Nakae, S., Doko, K., Tada, T., Shirai, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.289 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 S218D and S222D mutant

Nakae, S., Doko, K., Tada, T., Shirai, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 159.25 kDa 
• Atom Count: 9,265 
• Modeled Residue Count: 1,205 
• Deposited Residue Count: 1,400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase 1, isoform CRA_d	A, B, C, D	350	Homo sapiens	Mutation(s): 4  Gene Names: MAP2K1, hCG_24510 EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens) Explore Q02750  Go to UniProtKB:  Q02750
PHAROS:  Q02750 GTEx:  ENSG00000169032

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A], G [auth B], H [auth C], J [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	F [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.289 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.17	α = 90
b = 132.55	β = 90
c = 91.21	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Nakae, S., Doko, K., Tada, T., Shirai, T.

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Funding Organization	Location	Grant Number
		26440035

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Data collection
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description