Structure of PDB 6why Chain A

Receptor sequence

>6whyA (length=790) Species: 10116 (Rattus norvegicus)

KIVNIGAVLSTRKHEQMFREAVNQANKRIQLQATSVTHKPNAIQMALSVC
EDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYS
DKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKR
LETLLEEREGPKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDA
ATVYRAAAMLDMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNES
AHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSS
KYADGVTGRVEFNEDGDRKFAQYSIMNLQNRKLVQVGIYNGTHVIPNDRK
IIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNG
DPVKKVICTGPNDRHTVPQCCYGFCIDLLIKLARTMQFTYEVHLVADGKF
GTQERVQNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFK
YQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFS
TLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANL
AAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELST
MYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGE
LFFRSGFGIGMRKDSPWKQQVSLSILKSHENGFMEDLDKTWVRYQECDSR
SNAPATLTCENMAGVFMLVAGGIVAGIFLIFIEIAYKRHK

3D structure

• PDB: 6why Structural Basis of Functional Transitions in Mammalian NMDA Receptors.
• Chain: A
• Resolution: 4.03 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	QGM	A	Q426 P537 L538 T539 V705 K706 Q707 S708 W752	Q377 P482 L483 T484 V633 K634 Q635 S636 W680	BindingDB: Ki=6.3nM

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0015276 ligand-gated monoatomic ion channel activity
• GO:0038023 signaling receptor activity

Biological Process

• GO:0006811 monoatomic ion transport

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:6why, PDBe:6why, PDBj:6why
• PDBsum: 6why
• PubMed: 32610085
• UniProt: P35439|NMDZ1_RAT Glutamate receptor ionotropic, NMDA 1 (Gene Name=Grin1)