3GOK

Binding site mapping of protein ligands

PDB DOI: https://doi.org/10.2210/pdb3GOK/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2009-03-19 Released: 2010-03-02
Deposition Author(s): Scheich, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.258
R-Value Work: 0.238
R-Value Observed: 0.239

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 3,434
Deposited Residue Count: 4,008
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	334	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49137
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4O Query on P4O Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth K] mmCIF format, chain X [auth L]	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		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.258
R-Value Work: 0.238
R-Value Observed: 0.239
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.208	α = 90
b = 183.192	β = 90
c = 217.656	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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

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Deposit Data

Help and Resources

3GOK

Binding site mapping of protein ligands

Binding site mapping of protein ligands

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)