3GCP

Human P38 MAP Kinase in Complex with SB203580

PDB DOI: https://doi.org/10.2210/pdb3GCP/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-02-22 Released: 2009-06-09
Deposition Author(s): Gruetter, C., Simard, J.R., Rauh, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.276
R-Value Work: 0.197
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 42.2 kDa
Atom Count: 2,926
Modelled Residue Count: 337
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 4 Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539 Go to UniProtKB: Q16539
PHAROS: Q16539 GTEx: ENSG00000112062
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SB2 Query on SB2 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-3H-IMIDAZOL-4-YL]-PYRIDINE C₂₁ H₁₆ F N₃ O S CDMGBJANTYXAIV-MHZLTWQESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A]	C [auth A], D [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
SB2	Binding MOAD: 3GCP	Kd: 15 (nM) from 1 assay(s)
SB2	PDBBind: 3GCP	Kd: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.276
R-Value Work: 0.197
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.89	α = 90
b = 69.87	β = 90
c = 74.51	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Gruetter, C.

Simard, J.R.

Rauh, D.

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2021-10-20
Changes: Database references, Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description

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Deposit Data

Help and Resources

3GCP

Human P38 MAP Kinase in Complex with SB203580

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)