3KS9 | pdb_00003ks9

Metabotropic glutamate receptor mGluR1 complexed with LY341495 antagonist

PDB DOI: https://doi.org/10.2210/pdb3KS9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): Yes

Deposited: 2009-11-20 Released: 2009-12-08
Deposition Author(s): Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.241 (Depositor), 0.235 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Metabotropic glutamate receptor mglur1 complexed with LY341495 antagonist

Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A.

To be published.

Macromolecule Content

Total Structure Weight: 112.58 kDa
Atom Count: 7,727
Modeled Residue Count: 887
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 1	A, B	496	Homo sapiens	Mutation(s): 1 Gene Names: GPRC1A, GRM1, MGLUR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13255 (Homo sapiens) Explore Q13255 Go to UniProtKB: Q13255
PHAROS: Q13255 GTEx: ENSG00000152822
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13255
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q13255-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Z99 Query on Z99 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine C₂₀ H₁₉ N O₅ VLZBRVJVCCNPRJ-KPHUOKFYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
Z99	BindingDB: 3KS9	Ki: 6800 (nM) from 1 assay(s)
		IC50: min: 7800, max: 8990 (nM) from 2 assay(s)
		EC50: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241 (Depositor), 0.235 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.23	α = 90
b = 96.546	β = 106.67
c = 97.545	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2021-10-13
Changes: Database references, Structure summary
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description
Version 1.6: 2024-10-30
Changes: Structure summary