2NPT | pdb_00002npt

Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox domain (MAP2K5-phox) with human mitogen activated protein kinase kinase kinase 2 phox domain (MAP3K2-phox)

• PDB DOI: https://doi.org/10.2210/pdb2NPT/pdb

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


• Deposited: 2006-10-30 Released: 2006-11-28 
• Deposition Author(s): Filippakopoulos, P., Debreczeni, J., Papagrigoriou, V., Turnbull, A., Edwards, A., Arrowsmith, C., Sundstrom, M., von Delft, F., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox domain (MAP2K5-phox) with human mitogen activated protein kinase kinase kinase 2 phox domain (MAP3K2-phox)

Filippakopoulos, P., Debreczeni, J., Papagrigoriou, V., Turnbull, A., Edwards, A., Arrowsmith, C., Sundstrom, M., von Delft, F., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.95 kDa 
• Atom Count: 3,272 
• Modeled Residue Count: 375 
• Deposited Residue Count: 412 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 5	A, C	106	Homo sapiens	Mutation(s): 0  Gene Names: MAP2K5, MEK5, MKK5, PRKMK5 EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13163 (Homo sapiens) Explore Q13163  Go to UniProtKB:  Q13163
PHAROS:  Q13163 GTEx:  ENSG00000137764

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 2	B, D	100	Homo sapiens	Mutation(s): 0  Gene Names: MAP3K2, MAPKKK2, MEKK2 EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U5 (Homo sapiens) Explore Q9Y2U5  Go to UniProtKB:  Q9Y2U5
PHAROS:  Q9Y2U5 GTEx:  ENSG00000169967

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.333	α = 90
b = 61.41	β = 90
c = 143.651	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Filippakopoulos, P., Debreczeni, J., Papagrigoriou, V., Turnbull, A., Edwards, A., Arrowsmith, C., Sundstrom, M., von Delft, F., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description