6FMA | pdb_00006fma

Crystal structure of ERK2 in complex with an adenosine derivative

PDB DOI: https://doi.org/10.2210/pdb6FMA/pdb

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-01-30 Released: 2019-03-13
Deposition Author(s): Gelin, M., Labesse, G.
Funding Organization(s): FRISBI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.186 (Depositor), 0.186 (DCC)
R-Value Work:
0.143 (Depositor), 0.145 (DCC)
R-Value Observed:
0.145 (Depositor)

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

None

Gelin, M., Pochet, S., Labesse, G.

To be published.

Macromolecule Content

Total Structure Weight: 43.04 kDa
Atom Count: 3,275
Modeled Residue Count: 341
Deposited Residue Count: 364
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 1	A	364	Rattus norvegicus	Mutation(s): 0 Gene Names: Mapk1, Erk2, Mapk, Prkm1 EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086 Go to UniProtKB: P63086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63086
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DU8 Query on DU8 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]	3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanylpropanoic acid C₁₃ H₁₆ N₈ O₅ S HSUVCMYSEUNGIN-JJNLEZRASA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.186 (Depositor), 0.186 (DCC)
R-Value Work: 0.143 (Depositor), 0.145 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.66	α = 90
b = 70.04	β = 108.62
c = 59.64	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Gelin, M.

Labesse, G.

Funding Organization	Location	Grant Number
FRISBI	France	ANR-10-INSB-05

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary