3EQC

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a ternary complex with compound 1, ATP-GS AND MG2P

Structural Biology Knowledgebase: 3EQC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EQC

Classification: TRANSFERASE

Total Structure Weight: 41222.87

Macromolecule Entities
Molecule Chains Length Organism Details
Dual specificity mitogen-activated protein kinase kinase 1 A 360 Homo sapiens EC#: 2.7.12.2 IUBMB
Fragment: Protein kinase domain, UNP residues 35-393
Mutation: S298N, S299K, Y300F
Gene Name(s): MAP2K1 Gene View MEK1 PRKMK1

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AGS
Query on AGS

A PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'- (GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE (Synonym)
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3BM
Query on 3BM

A 2-[(2-chloro-4-iodophenyl)amino]-N-{[(2R)- 2,3-dihydroxypropyl]oxy}-3,4-difluorobenzamide
C16 H14 Cl F2 I N2 O4
FCADPEDUULETPK-SECBINFHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.199
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 77.22 α = 90.00
b = 77.22 β = 90.00
c = 222.05 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-30
  • Released Date: 2009-02-24
  • Deposition author(s): Fischmann, T.O.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4