3GOK | pdb_00003gok

Binding site mapping of protein ligands

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.258 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.238 (Depositor) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Binding site mapping of protein ligands

Scheich, C., Smith, M.A., Barker, J.D., Kahmann, J., Hesterkamp, T., Schade, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 464.02 kDa 
  • Atom Count: 28,332 
  • Modeled Residue Count: 3,434 
  • Deposited Residue Count: 4,008 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
334Homo sapiensMutation(s): 0 
Gene Names: 9261, MAPKAPK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49137 (Homo sapiens)
Explore P49137 
Go to UniProtKB:  P49137
PHAROS:  P49137
GTEx:  ENSG00000162889 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4O

Query on P4O


Download:Ideal Coordinates CCD File
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE
C21 H16 N4 O
OWFLADWRSCINST-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.258 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.238 (Depositor) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.208α = 90
b = 183.192β = 90
c = 217.656γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2010-03-02 
    • Deposition Author(s): Scheich, C.

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description