5TPW
Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A
- PDB DOI: https://doi.org/10.2210/pdb5TPW/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Xenopus laevis, Rattus norvegicus, Mus musculus
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2016-10-21 Released: 2016-12-14 
- Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.91 Å
- R-Value Free: 0.245 
- R-Value Work: 0.200 
- R-Value Observed: 0.204 
This is version 1.5 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 | 389 | 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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate receptor ionotropic, NMDA 2A | 360 | Rattus norvegicus | Mutation(s): 0  Gene Names: Grin2a | ||
UniProt | |||||
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959  Go to UniProtKB:  Q00959 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q00959 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
FAB, HEAVY CHAIN | C [auth H] | 221 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
FAB, LIGHT CHAIN | D [auth L] | 214 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A], F [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | G [auth A] H [auth A] I [auth A] M [auth B] N [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | J [auth A], K [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ZN Query on ZN | L [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.91 Å
- R-Value Free: 0.245 
- R-Value Work: 0.200 
- R-Value Observed: 0.204 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 79.56 | α = 90 |
b = 118.401 | β = 90 |
c = 155.812 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
PHENIX | model building |
PDB_EXTRACT | data extraction |
PHASER | phasing |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-12-14  Deposition Author(s): Romero-Hernandez, A., Simorowski, N., Karakas, E., Furukawa, H.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) | United States | MH085926 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM105730 |
Revision History (Full details and data files)
- Version 1.0: 2016-12-14
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Refinement description - Version 1.2: 2018-05-16
Changes: Data collection, Database references - Version 1.3: 2019-11-27
Changes: Author supporting evidence - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary