3VVH | pdb_00003vvh

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP

• PDB DOI: https://doi.org/10.2210/pdb3VVH/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-24 Released: 2013-08-28 
• Deposition Author(s): Kudo, N., Kato, R., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP

Kudo, N., Kato, R., Wakatsuki, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.83 kDa 
• Atom Count: 7,168 
• Modeled Residue Count: 860 
• Deposited Residue Count: 1,023 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 1	A, B, C	341	Homo sapiens	Mutation(s): 0  Gene Names: MAP2K1, MEK1, PRKMK1 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], H [auth B], K [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
4BM	F [auth A], I [auth B], L [auth C]	N-{[(2R)-2,3-dihydroxypropyl]oxy}-3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]benzamide C16 H14 F3 I N2 O4 SUDAHWBOROXANE-SECBINFHSA-N
MG	D [auth A], G [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4BM	BindingDB:  3VVH	Kd: min: 0.4, max: 100 (nM) from 4 assay(s)
		IC50: min: 0.33, max: 110 (nM) from 12 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.894	α = 90
b = 129.09	β = 90
c = 135.736	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Kudo, N., Kato, R., Wakatsuki, S.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description