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 
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 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
NMDA glutamate receptor subunit | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate receptor ionotropic, NMDA 2B | 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 AnnotationsExpand | |||||
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Oligosaccharides
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 | ||
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 | J [auth B], O [auth D] | 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol C21 H27 N O2 UYNVMODNBIQBMV-KKSFZXQISA-N | |||
NAG Query on NAG | G [auth A] H [auth B] I [auth B] L [auth C] M [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
NA Query on NA | F [auth A], K [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
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 Name | Purpose |
---|---|
BUSTER-TNT | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
BUSTER | phasing |
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