spacer
spacer

PDBsum entry 4h3p

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
4h3p
Jmol
Contents
Protein chains
342 a.a.
16 a.a.
17 a.a.
Ligands
ANP ×2
Waters ×177
PDB id:
4h3p
Name: Transferase
Title: Crystal structure of human erk2 complexed with a mapk dockin
Structure: Mitogen-activated protein kinase 1. Chain: a, d. Fragment: kinase domain. Synonym: map kinase 1, mapk 1, ert1, extracellular signal-r kinase 2, erk-2, map kinase isoform p42, p42-mapk, mitogen- protein kinase 2, map kinase 2, mapk 2. Engineered: yes. Mutation: yes. Ribosomal protein s6 kinase alpha-1.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: mapk1, erk2, prkm1, prkm2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic construct
Resolution:
2.30Å     R-factor:   0.180     R-free:   0.224
Authors: G.Gogl,I.Toeroe,A.Remenyi
Key ref: G.Gógl et al. (2013). Protein-peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase. Acta Crystallogr D Biol Crystallogr, 69, 486-489. PubMed id: 23519423 DOI: 10.1107/S0907444912051062
Date:
14-Sep-12     Release date:   27-Feb-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28482  (MK01_HUMAN) -  Mitogen-activated protein kinase 1
Seq:
Struc:
360 a.a.
342 a.a.*
Protein chain
Pfam   ArchSchema ?
Q15418  (KS6A1_HUMAN) -  Ribosomal protein S6 kinase alpha-1
Seq:
Struc:
 
Seq:
Struc:
735 a.a.
16 a.a.*
Protein chain
Pfam   ArchSchema ?
Q15418  (KS6A1_HUMAN) -  Ribosomal protein S6 kinase alpha-1
Seq:
Struc:
 
Seq:
Struc:
735 a.a.
17 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains A, D: E.C.2.7.11.24  - Mitogen-activated protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphoprotein
   Enzyme class 3: Chains B, E: E.C.2.7.11.1  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphoprotein
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   21 terms 
  Biological process     viral reproduction   73 terms 
  Biochemical function     nucleotide binding     15 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444912051062 Acta Crystallogr D Biol Crystallogr 69:486-489 (2013)
PubMed id: 23519423  
 
 
Protein-peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase.
G.Gógl, I.Törő, A.Reményi.
 
  ABSTRACT  
 
Linear motifs normally bind with only medium binding affinity (Kd of ∼0.1-10 µM) to shallow protein-interaction surfaces on their binding partners. The crystallization of proteins in complex with linear motif-containing peptides is often challenging because the energy gained upon crystal packing between symmetry mates in the crystal may be on a par with the binding energy of the protein-peptide complex. Furthermore, for extracellular signal-regulated kinase 2 (ERK2) the protein-peptide docking surface is comprised of a small hydrophobic surface patch that is often engaged in the crystal packing of apo ERK2 crystals. Here, a rational surface-engineering approach is presented that involves mutating protein surface residues that are distant from the peptide-binding ERK2 docking groove to alanines. These ERK2 surface mutations decrease the chance of `unwanted' crystal packing of ERK2 and the approach led to the structure determination of ERK2 in complex with new docking peptides. These findings highlight the importance of negative selection in crystal engineering for weakly binding protein-peptide complexes.