Macromolecule Content

Total Structure Weight: 116.83 kDa
Atom Count: 7168
Modelled Residue Count: 860
Deposited Residue Count: 1023
Unique protein chains: 1

3VVH

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

DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225
R-Value Work: 0.198
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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
Find proteins for Q02750 (Homo sapiens) Explore Q02750 Go to UniProtKB: Q02750
NIH Common Fund Data Resources
PHAROS: Q02750 GTEx: ENSG00000169032
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain H [B] SDF format, chain K [C] MOL2 format, chain E [A] MOL2 format, chain H [B] MOL2 format, chain K [C]	A, B, C	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Ligand Interaction
4BM Query on 4BM Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain I [B] SDF format, chain L [C] MOL2 format, chain F [A] MOL2 format, chain I [B] MOL2 format, chain L [C]	A, B, 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		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain G [B] SDF format, chain J [C] MOL2 format, chain D [A] MOL2 format, chain G [B] MOL2 format, chain J [C]	A, B, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4BM	Kd: 0.4000000059604645 nM BindingDB
4BM	Kd: 31 nM BindingDB
4BM	IC50: 13 nM BindingDB
4BM	IC50: 15 nM BindingDB
4BM	IC50: 0.6000000238418579 nM BindingDB
4BM	IC50: 7 nM BindingDB
4BM	IC50: 0.33000001311302185 nM BindingDB
4BM	IC50: 5.199999809265137 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225
R-Value Work: 0.198
R-Value Observed: 0.199
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2012-07-24
Released Date: 2013-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.