3FVO | pdb_00003fvo

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-epi-neodysiherbaine A in space group P1

PDB DOI: https://doi.org/10.2210/pdb3FVO/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-16 Released: 2010-01-19
Deposition Author(s): Unno, M., Sasaki, M., Ikeda-Saito, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.191 (Depositor), 0.201 (DCC)
R-Value Work:
0.165 (Depositor), 0.182 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structures of Human GluR5 Ligand-Binding Core in Complexes with Novel Marine-Derived Toxins, Dysiherbaine and Neodysiherbaine A, and Their Analogues

Unno, M., Shinohara, M., Takayama, K., Teruya, K., Doh-ura, K., Sakai, R., Sasaki, M., Ikeda-Saito, M.

To be published.

Macromolecule Content

Total Structure Weight: 60.07 kDa
Atom Count: 4,835
Modeled Residue Count: 512
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor, ionotropic kainate 1	A, B	256	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P39086 (Homo sapiens) Explore P39086 Go to UniProtKB: P39086
PHAROS: P39086 GTEx: ENSG00000171189
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39086
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8EP Query on 8EP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	(2R,3aR,6R,7S,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-6,7-dihydroxy-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid C₁₁ H₁₇ N O₈ NRTJEXLNSCGBJU-JROTZIKASA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B]
GOL Query on GOL 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] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] J [auth B] C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.191 (Depositor), 0.201 (DCC)
R-Value Work: 0.165 (Depositor), 0.182 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.717	α = 94.19
b = 50.756	β = 95.9
c = 63.29	γ = 117.95

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Unno, M.

Sasaki, M.

Ikeda-Saito, M.

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-16
Changes: Refinement description, Source and taxonomy
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary

3FVO | pdb_00003fvo

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-epi-neodysiherbaine A in space group P1

Literature

Crystal Structures of Human GluR5 Ligand-Binding Core in Complexes with Novel Marine-Derived Toxins, Dysiherbaine and Neodysiherbaine A, and Their Analogues

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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