5EWJ

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL

PDB DOI: https://doi.org/10.2210/pdb5EWJ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Xenopus laevis, Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2015-11-20 Released: 2016-03-02
Deposition Author(s): Pandit, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.211
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 173.15 kDa
Atom Count: 11,563
Modelled Residue Count: 1,421
Deposited Residue Count: 1,508
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NMDA glutamate receptor subunit	A, C	390	Xenopus laevis	Mutation(s): 2 Gene Names: grin1, NR1
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis) Explore A0A1L8F5J9 Go to UniProtKB: A0A1L8F5J9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L8F5J9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2B	B, D	364	Homo sapiens	Mutation(s): 1 Gene Names: GRIN2B, NMDAR2B
UniProt & NIH Common Fund Data Resources
Find proteins for Q13224 (Homo sapiens) Explore Q13224 Go to UniProtKB: Q13224
PHAROS: Q13224 GTEx: ENSG00000273079
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13224
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QEL Query on QEL Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B]	J [auth B], O [auth D]	4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol C₂₁ H₂₇ N O₂ UYNVMODNBIQBMV-KKSFZXQISA-N		Interactions Focus chain J [auth B] Focus chain O [auth D] Interactions & Density Focus chain J [auth B] Focus chain O [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	G [auth A] H [auth B] I [auth B] L [auth C] M [auth D] G [auth A], H [auth B], I [auth B], L [auth C], M [auth D], N [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain F [auth A]	F [auth A], K [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
QEL	BindingDB: 5EWJ	Ki: min: 10, max: 29 (nM) from 6 assay(s)
		Kd: min: 7.6, max: 94 (nM) from 2 assay(s)
		IC50: min: 20, max: 340 (nM) from 9 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.211
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 268.46	α = 90
b = 60.1	β = 116.22
c = 145	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Pandit, J.

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2016-03-09
Changes: Database references
Version 1.2: 2016-04-13
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary