6Y82 | pdb_00006y82

Fragment KCL_804 in complex with MAP kinase p38-alpha

PDB DOI: https://doi.org/10.2210/pdb6Y82/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-03-03 Released: 2020-03-11
Deposition Author(s): De Nicola, G.F., Nichols, C.E.
Funding Organization(s): British Heart Foundation, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.243 (Depositor), 0.241 (DCC)
R-Value Work:
0.216 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fragment KCL_804 in complex with MAP kinase p38-alpha

De Nicola, G.F., Nichols, C.E.

To be published.

Macromolecule Content

Total Structure Weight: 41.97 kDa
Atom Count: 3,124
Modeled Residue Count: 348
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Mus musculus	Mutation(s): 1 Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811 Go to UniProtKB: P47811
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SB4 Query on SB4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE C₁₈ H₁₉ F N₆ VSPFURGQAYMVAN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
308 (Subject of Investigation/LOI) Query on 308 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine C₁₀ H₁₇ N DKNWSYNQZKUICI-CHIWXEEVSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.243 (Depositor), 0.241 (DCC)
R-Value Work: 0.216 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.918	α = 90
b = 102.289	β = 90
c = 102.944	γ = 90

Software Package:

Software Name	Purpose
DIALS	data collection
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

De Nicola, G.F.

Nichols, C.E.

Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	SP/14/2/30922, FS/14/29/30896
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_PC_17164

Revision History (Full details and data files)

Version 1.0: 2020-03-11
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description