Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors
Regan, M.C., Furukawa, H.(2019) Nat Commun 10: 321
Experimental Data Snapshot
Starting Model: experimental
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(2019) Nat Commun 10: 321
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate receptor ionotropic, NMDA 1 | 385 | Xenopus laevis | Mutation(s): 2  Gene Names: grin1 Membrane Entity: Yes  | ![]() | |
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 | ||||
Glycosylation | |||||
Glycosylation Sites: 3 | |||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate receptor ionotropic, NMDA 2B | 363 | Rattus norvegicus | Mutation(s): 1  Gene Names: Grin2b Membrane Entity: Yes  | ![]() | |
UniProt | |||||
Find proteins for Q00960 (Rattus norvegicus) Explore Q00960  Go to UniProtKB:  Q00960 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q00960 | ||||
Glycosylation | |||||
Glycosylation Sites: 1 | Go to GlyGen: Q00960-1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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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 |
Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
T88 (Subject of Investigation/LOI) Query on T88 | L [auth B], V [auth D] | N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide C22 H30 Cl2 N2 O4 S NHYMWKHINJIWJL-LJQANCHMSA-N | |||
NAG Query on NAG | F [auth A], G [auth A], K [auth B], Q [auth C], R [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | I [auth A] J [auth A] M [auth B] N [auth B] O [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | H [auth A], S [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Length ( Å ) | Angle ( ˚ ) |
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a = 268.131 | α = 90 |
b = 59.612 | β = 116.86 |
c = 145.526 | γ = 90 |
Software Name | Purpose |
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HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
PHASER | phasing |
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) | United States | F32NS093753 |
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) | United States | R01MH085926 |